P0339 on 2013-2016 Honda Accord: Crankshaft Sensor Intermittent Signal Causes and Fixes

What's Unique About the 2013-2016 Honda ACCORD

For this generation of Honda Accord (9th Gen) and its platform mates like the CR-V, the P0339 code is a well-documented issue. Honda released Technical Service Bulletin (TSB) A16-011 specifically for 2013-2016 models, identifying corrosion between the engine wire harness and the CKP sensor connector as a primary cause. Unlike a simple sensor failure, this TSB indicates the problem is often the connection itself. The official corrective action listed in the TSB is to replace both the CKP sensor and the entire engine wire harness, which is a much more involved repair than just replacing the sensor.

Diagnostic Flowchart

Tap your situation to follow the diagnostic path that matches what you're seeing on this vehicle.

Symptoms You May Notice

• Check Engine Light is on
• Engine stalls intermittently, especially while driving or coming to a stop
• Difficulty starting the engine, or multiple attempts needed to start 🎬 See how a faulty sensor causes these starting issues. (long crank)
• Engine cranks but does not start/ignite
• Rough or uneven idle
• Engine misfires, sometimes triggering codes P0300-P0304
• Hesitation or stumbling during acceleration
• Reduced fuel economy
• Vehicle enters 'limp mode' with severely reduced power

Most Likely Causes

1. Corroded or Damaged CKP Sensor Connector/Wiring 🔴 High Probability Honda TSB A16-011 and SB16011 specifically call out corrosion at the CKP sensor connector as a known issue on these models, leading to P0339. The sensor's location on the lower engine block exposes it to road salt and moisture.
   How to confirm: Visually inspect the crankshaft position sensor's electrical connector for any signs of corrosion (green or white powder), moisture, or damaged/loose pins. Wiggle the connector and wiring with the engine running (if possible) to see if it causes stalling or a change in engine behavior.
   Typical fix: Clean the connector terminals thoroughly with an electrical contact cleaner. If corrosion is severe or the connector is damaged, it may need to be replaced. The official fix per TSB 16-011 is to replace both the CKP sensor and the entire engine wire harness.
   Est. part cost: $5-$30 for a connector pigtail, $400+ for an engine wire harness.
2. Failing Crankshaft Position (CKP) Sensor 🔴 High Probability The sensor operates in a high-heat, high-vibration environment on the engine block, leading to eventual failure over time. Owner forums are filled with stories of aftermarket sensors failing quickly, making OEM sensors (Denso, Hitachi, or Honda-branded) highly recommended.
   How to confirm: If the wiring and connector are confirmed to be in good condition, the sensor itself is the next likely culprit. A definitive test involves monitoring the sensor's output signal with an oscilloscope for dropouts. For most DIYers, replacing the sensor with a quality OEM part is a common and effective diagnostic step after checking the wiring.
   Typical fix: Replace the crankshaft position sensor. A 'CKP Pattern Learn' procedure with a compatible scan tool is required after replacement to ensure the ECM correctly reads the new sensor and to prevent the code from returning. Failure to perform this step is a common reason for the fix not working.
   Est. part cost: $30-$100 for aftermarket, $130-$165 for OEM.

Rare But Worth Checking

• Damaged Reluctor Wheel/Timing Ring: The CKP sensor reads teeth on a ring (reluctor) to determine crankshaft position. If this ring is damaged, bent, or has debris on it, it can cause an erratic signal. This is rare and typically only happens if there has been other major engine work or damage.
• Failing Powertrain Control Module (PCM): In very rare instances, the fault may lie within the engine computer itself. This should only be considered after all other possibilities (sensor, wiring, connectors) have been thoroughly ruled out.
• Blown Fuse: On some Honda models, the crankshaft position sensor may share a circuit and fuse with the camshaft position sensor. A short in the wiring for either sensor could blow the fuse, causing a loss of signal.

Diagnosis Steps

1. Read the trouble codes with an OBD-II scanner. Confirm P0339 is present and note any other codes, especially P0335 or misfire codes (P030x).
2. Locate the crankshaft position sensor. On the 2.4L 4-cylinder, it's on the lower part of the engine block, near the oil pan and exhaust, 🎬 Watch: Locate and replace the sensor on a 9th Gen Accord. behind a small heat shield. On the 3.5L V6, it is more difficult to access, located behind the timing belt cover.
3. Perform a thorough visual inspection of the CKP sensor's connector and wiring harness. Look for corrosion, loose pins, or damage, as highlighted in Honda TSB A16-011.
4. Check for a related blown fuse in the under-hood or interior fuse box.
5. If corrosion is found, disconnect the battery, then clean the connector and sensor pins using electrical contact cleaner and a small brush. Ensure a secure connection when re-plugging. If the problem returns, the harness may be compromised internally.
6. If the connector is clean and the problem persists, the next step is to replace the CKP sensor, preferably with an OEM part.
7. After replacing the sensor, clear the trouble codes.
8. Perform a 'CKP Pattern Learn' procedure using a compatible bidirectional scan tool or the manual relearn process. This step is crucial for preventing the code from returning and ensuring smooth engine operation. Failure to do this is a common reason for the fix not working.
9. If the code returns after these steps, the wiring harness should be tested for continuity and shorts, or you may need to consult a professional to investigate a rare cause like a damaged reluctor ring or faulty PCM, or to perform the full TSB A16-011 procedure (harness replacement).

Parts You'll Likely Need

• Crankshaft Position Sensor (OEM #37500-R40-A01) — This is the sensor that generates the signal the ECM is reporting as intermittent. It is the most common point of failure for this code after wiring issues are ruled out. TSB A16-011 also lists part number 37500-R60-U01 as a replacement.
  Trusted brands: Denso (OEM supplier), Hitachi (OEM supplier), Honda (Genuine), NGK/NTK
  OEM price range: $130-$165
  Aftermarket price range: $30-$90
• Engine Wire Harness (2.4L M/T) (OEM #32110-5A2-306) — Required for the official TSB A16-011 fix if corrosion is severe. This part is for 2014-16 models with a manual transmission.
  Trusted brands: Honda (Genuine)
  OEM price range: $400-$500
  Aftermarket price range: N/A
• Engine Wire Harness (2.4L CVT) (OEM #32110-5A2-406) — Required for the official TSB A16-011 fix if corrosion is severe. This part is for 2014-16 models with a CVT transmission.
  Trusted brands: Honda (Genuine)
  OEM price range: $400-$500
  Aftermarket price range: N/A

Related Codes That Often Appear With This One

• P0335 — P0335 means 'CKP Sensor No Signal'. It often appears with P0339 because a sensor that is failing intermittently (P0339) may eventually fail completely (P0335). The official Honda TSBs mention both codes occurring together.
• P0300, P0301, P0302, P0303, P0304 — These are random or specific cylinder misfire codes. An intermittent CKP signal disrupts the PCM's ability to accurately time ignition and fuel injection, which can lead to misfires.

Technical Service Bulletins (TSBs) & Recalls

• A16-011: MIL Comes on with DTC P0335 and/or P0339

Platform-Specific Known Issues

• Honda Technical Service Bulletin (TSB) #A16-011 was issued for 2013-2016 Accords (and 2015-16 CR-V), specifically mentioning that corrosion in the CKP sensor connector can cause DTC P0335 and/or P0339. The official fix involves replacing the sensor AND the entire engine wire harness.
• Owner Experience: A user on Reddit with an '08 Accord (experiencing a similar known issue) detailed a frustrating cycle of replacing the sensor with aftermarket parts, having the code return, and multiple trips to the dealer. The issue persisted until an OEM sensor was used and the PCM was updated, highlighting the sensitivity of the system to part quality and software.
• Owner Experience: A user on a Honda-Tech forum with a 2011 CR-V (platform mate) described replacing the CKP sensor with two different aftermarket brands, only to have the P0339 code and starting issues continue to return intermittently. This reinforces the idea that wiring issues or faulty new parts can mimic the original failure.

Mechanic-Grade Diagnostic Values

• CKP Sensor Live Data (Scan Tool) — expected: 100-500 RPM while cranking engine.. Failure: A reading of 0 RPM while the engine is cranking indicates a likely failed sensor or circuit.
• CKP Sensor Resistance (3-wire Hall Effect type) — expected: Resistance tests are not a reliable indicator for Hall Effect sensors.. Failure: N/A. Voltage testing is preferred.
• CKP Sensor Connector Voltage (Key On, Engine Off) — expected: On the 3-pin connector: one pin should have ~5V (reference voltage from PCM), one pin should have near 0V (ground), and the third is the signal wire.. Failure: Absence of the 5V reference or a bad ground points to a wiring or PCM issue, not necessarily a bad sensor.

Scan Tool Commands That Help

• Honda HDS (or capable aftermarket scanner): CKP PATTERN CLEAR — This must be performed before the 'Learn' procedure. It erases the stored CKP pattern from the PCM, which is necessary after replacing the sensor or performing major engine work.
• Honda HDS (or capable aftermarket scanner): CKP PATTERN LEARN / LEARNING — This is used after replacing the CKP sensor or clearing the old pattern. The PCM learns the specific pattern of the new sensor's reluctor wheel to ensure accurate timing. Failure to perform this is a common reason the P0339 code returns after a repair.
• Manual Procedure (No Scan Tool): Manual CKP Pattern Learn — If a compatible scan tool is unavailable. After warming the engine up (radiator fan cycles on), decelerate with the throttle fully closed from 2,500 RPM to 1,000 RPM in a low gear (1st for M/T, 2 for A/T). Repeat several times.

Wiring & Ground Locations

• G101 — On the intake manifold, typically on the driver's side of the engine bay.. This is a primary ground point for the engine control system and its sensors. A poor connection at G101 can cause a host of intermittent electrical issues, including erratic sensor signals that could trigger a P0339 code.
• CKP Sensor Connector — On the 2.4L, it's on the lower front of the engine block, near the crankshaft pulley/oil pan area. On the 3.5L V6, it's behind the timing belt cover.. This is the direct connection point for the sensor. Honda TSB A16-011 specifically identifies corrosion at this connector as a primary cause of P0339 on these vehicles.

Real Owner Repair Stories

• YouTube user 'my C.A.R.S' (Honda (model unspecified, but K-series engine similar to Accord)) — Car takes 10-15 seconds of cranking to start, P0339 code stored.
  ❌ Tried (didn't work) Initial diagnosis pointed to a bad sensor.
  ✅ What actually fixed it The crankshaft reluctor wheel (pulse plate) had been installed backward during a previous timing chain replacement. The wheel is marked with 'OUTSIDE' and must face away from the engine block. Flipping the wheel to the correct orientation resolved the long crank and the code.
• Honda-Tech forum user (2010 Honda Accord 2.4L) — Long crank when warm, eventually stored P0339 and P0302 (misfire).
  ❌ Tried (didn't work) Replacing the original starter with a TYC aftermarket starter., Replacing the aftermarket starter with a rebuilt Mitsuba starter.
  ✅ What actually fixed it The user replaced the crankshaft position sensor with a new OEM part and performed the manual relearn procedure (decelerating from 3k RPM). After the relearn, the check engine light cleared and full power was restored. The user suspects the aftermarket starter may have created electrical noise that triggered the initial P0339 code.

When the Usual Fixes Don't Work

• While the most common fixes for P0339 are cleaning the connector or replacing the CKP sensor, there are documented cases where the true cause was far less obvious. In one instance, a P0339 code with a long-crank symptom was only resolved after discovering the crankshaft's reluctor wheel had been installed backward during a prior timing chain service. No amount of sensor replacements or wiring checks would have fixed this mechanical error. In another case, the P0339 code appeared after an aftermarket starter was installed; the ultimate fix was an OEM sensor and a relearn, but the catalyst appeared to be electrical noise from the non-OEM starter. These cases show that if the standard fixes fail, the diagnostic path must expand to include mechanical history and interference from seemingly unrelated components.

OEM Part Supersession History

• 37500-R40-A01 → 37500-R60-U01 (per TSB A16-011) — The TSB specifies a new part number to be used in conjunction with the engine wire harness replacement, likely an updated design to improve resistance to the corrosion issue.
  Heads up: While 37500-R40-A01 is still widely sold and fits, the TSB procedure specifically calls for the 37500-R60-U01 part when performing the full harness replacement fix.

Model Year Variations Within This Range

• 2013-2016: The 2016 model year received a significant facelift with updated styling, a more rigid chassis, and new infotainment features. However, the core powertrain options (2.4L K24W1 and 3.5L J35Y series engines) and the associated engine management electronics, including the crankshaft position sensor, remained fundamentally the same. Therefore, the causes and repair procedures for code P0339 are consistent across the entire 2013-2016 model year range.