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5th Gen 4Runner: Rough idle, shaking, or misfire with a flashing check engine light

Safety: A flashing check engine light means active misfire that can overheat and damage the catalytic converter. Reduce load and get it checked soon.

Checks, in order

  1. Scan for the cylinder
    A basic OBD2 reader will show P0301 to P0306 for the misfiring cylinder, or P0300 for random. Cylinders 1, 3, 5 are one bank and 2, 4, 6 the other, which helps narrow it down.
    easy $ · under about $50
  2. Spark plugs
    Pull the plugs and check the gap and condition. High-mileage trucks past the service interval are a common fix, and iridium plugs are the normal type here.
    medium $ · under about $50
  3. Swap coils between cylinders
    Move the coil from the misfiring cylinder to another one and clear the code. If the misfire follows the coil, replace that coil.
    easy $$ · about $50 to $500
  4. Look for oil in the plug wells
    While the coils are out, check the tubes for oil. A leaking tube seal will foul the plug and boot and cause repeat misfires until it is resealed.
    medium $$ · about $50 to $500
  5. Vacuum leaks and fuel delivery
    Listen for hissing, inspect the intake boot and brake booster hose, and note if the idle changes with the hood open. If every cylinder is affected, test fuel pressure before blaming the ignition.
    medium $$ · about $50 to $500

Applies to: 5th generation 4Runner, 2010 to 2024, with the 1GR-FE 4.0L V6 and the 5-speed automatic. Assumes the stock configuration; trim-specific items (KDSS, sunroof, A/C) are noted where they apply.

Tools and parts for these checks

Links below are Amazon affiliate links: as an Amazon Associate, toyotadata earns from qualifying purchases, at no extra cost to you. Confirm fitment for your exact truck before you order.

ITEMUSED FORBUY
Bluetooth OBD2 scanner with live dataReading and clearing codes and watching live sensor dataShop on Amazon
Ignition coilSwapping a suspect coil after the misfire follows itShop on Amazon
Spark plugsReplacing worn plugs at the factory intervalShop on Amazon

Go deeper

The same problem on other Toyotas

More 5th Gen 4Runner problems

All 16 5th Gen 4Runner symptoms in the interactive troubleshooter →

General guidance from owner experience. Confirm torque specs, fluid capacities and procedures in the factory service manual. Brakes, steering and anything structural: if in doubt, have a qualified shop inspect it before driving.