Which parts fail
Components named in complaints (automatic and manual transmissions, CVT, axles, driveshaft, 4WD/AWD).
Mileage when the problem started
Owner reports
Selected complaints filed with NHTSA by 1999 Toyota 4Runner owners, lightly cleaned up (personal details are redacted by NHTSA).
The vehicle stalls, incosistently, but, on a frequent basis, at any given time, then will be fine for a long period of time. It eats batteries. I've had to replace the battery every year. A local automotive electrical specialist replaced the b+ cable from the battery to the starter, and the problem went away for a year, but, has since returned. I recently upgraded to a battery with more cranking watts, and have een improvement. However. There's the issue of the hesitation, jerking, and loss of power, when taking off after 1st start of the day, replaced plugs, and battery and did a tune - up, but, it made no difference. …
1999 Toyota 4runner, the left rear wheel axle seal is leaking gear oil all over the left rear wheel and brake. I have had the rear axle seals replaced 5 - 7 times: December 2006, June 2007, December 2007, June 2008, December 2008, and now again it is leaking February 2010. The independent auto repair business where I take my vehicle subscribes to "all data' which assists mechanics all over the country in sharing work done on vehicles; assisting in diagnosing similar problems, etc. There are a tremendous number of similar left rear axle seal failures on Toyota 4-runners and pickups 1999 - 2001 which use the same axle listed in the all data web site. Many of these list multiple times the seal as failed on the same vehicle. . I my case we have been getting the seals from Toyota. …
The rear axle seals repeatedly fail on this vehicle, I'm now having to make a fourth costly replacement of both the rear axle seal and contaminated brake shoes. For the fourth time the rear axle seal has failed which leaks brake fluid onto rear brake shoes, resulting in severe reduction of rear braking power. Also, as a result the front brakes are placed under undue pressure and warping of front brake rotors occurs which must also be addressed. While I have previously filed complaints over this same issue since 2005 with both Toyota and the nhtsb, there has been no recall initiated. The last time my rear axle seals were replaced was less than 20,000 miles ago. This vehicle only sees normal wear and usage. I am not the only complaint as many others have experienced the same issue based on Toyota forum discussions and a search of nhtsb complaint filings. …
Rear axle housing develops premature and detrimental metal scaling and rust, causing differential bell housing to leak gear oil. This problem has been reported on a significant number of 1999 through 2002 4runners in a consistent manner and pattern. Toyota motors has failed to acknowledge or research the problem and uses the defense that these vehicles are outside of warranty period. However, a consistent pattern of quality in this particular problem should warrant an investigation by NHTSA as Toyota has been shown to hide and distort claims by their loyal customer in order to cover up these types of problems. Please see http://www.4runnerforum.com/forum/showthread.php?t=1948 for one of the many threads related to this topic that demonstrates that the problem is persistent and Toyota has failed to recognize it.
Rear axle housing develops premature and detrimental metal scaling and rust, causing differential bell housing to leak gear oil. This problem has been reported on a significant number of 1999 through 2002 4runners in a consistent manner and pattern. Toyota motors has failed to acknowledge or research the problem and uses the defense that these vehicles are outside of warranty period. However, a consistent pattern of quality in this particular problem should warrant an investigation by NHTSA as Toyota has been shown to hide and distort claims by their loyal customer in order to cover up these types of problems. Please see http://www.4runnerforum.com/forum/showthread.php?t=1948 for one of the many threads related to this topic that demonstrates that the problem is persistent and Toyota has failed to recognize it.
I have a 1999 Toyota 4runner. Back in September 2009 the gas pedal got stuck at full throttle while I was driving it. I applied the brakes - pulled over and turned off the key. It scared me to death. My dad looked at it and found that the throttle cable plastic coating was coming apart and got stuck in the cable shielding. I called Toyota and they said it would cost around $300 to replace the defective cable. Is this a common problem with 1999 Toyota 4runners? Since this is definitely a safety issue, why won't Toyota fix it at their expense? I contacted turner Toyota in montrose colorado and talked to [redacted] in the service department. [redacted]
While driving from baltimore to washington d.c. On I-95 spd approx 65 MPH. My 1999 Toyota 4runner, started shaking violently. Suddenly I heard a loud crash, the clutch pedal went to the floor, and I almost lost control of the vehicle. I cautiously moved the vehicle over to the shoulder of the road, and come to find that my transmission had literally fell out from under the 4runner. Even the transfer case fell off the vehicle. I have all of my maintanence records, and the toyta dealership that serviced my vehicle refused to take responsibility, telling me that my vehicle was OK, then it breaking. Even Toyota corp. Will not even consider any assistance helping with my vehicle. What should I do?
My truck was being driven on a long trip. The differential starting making a whining noise that got louder and louder. I stopped at an oil change place at my destination to have them check the fluid. It was almost empty. Topped it up and chanced driving it 400 miles back to chicago. I made it OK and had mechanic look at it. The differential was so rusted that it had holes that allowed it to leak. The mechanic tried to find a used one but they all had the same problem. An internet search turned up countless examples of rusted differentials on Toyota trucks spanning many years. There is also extensive rusting on the frame, axle spare tire mount. This is obviously a long term Toyota problem.
Have a 1999 4runner which suffered right rear axle gasket failure at 59000 miles. Same 4runner suffered left rear axle gasket failure at 110000 miles. Have owned several 4runners (different years) that have never had rear axle problems. Has anyone else had same problem. Both problems were diagnosed at dealer and were considered safety hazards because grease was leaking onto rear brake pads. Would advise other owners of this year to have rear axle seals examined by dealer for same problem. Others have had same problem and have posted rear axle seal failures on www.Toyota-4runner.org.
My 1999 Toyota 4 runner has a severe issue with a rotted out frame. I was simply backing out of my driveway and came to a halt when I heard a thump. As I preceded to drive the vehicle it became apparent the backend was not responding well. I could feel the back end swaying and it felt as if there was an issue with the suspension. I took it in for inspection and was told the frame had rotted out right where the springs attach to the frame on the left hand side of the frame. The right side is rotted as well but the frame is still attached.
Transmission complaints in other 4Runner years
Frequently asked questions
How common are transmission problems on the 1999 Toyota 4Runner?
NHTSA has 23 complaints about the transmission & drivetrain of the 1999 Toyota 4Runner, 7% of the model year's 330 complaints. The component named most often is axle assembly (2 mentions).
Is there a recall for 1999 Toyota 4Runner transmission problems?
No. NHTSA lists no transmission & drivetrain recall for the 1999 Toyota 4Runner. If the problem is widespread, a repair may still be covered by an extended warranty or a manufacturer service bulletin — ask a dealer.
At what mileage do 1999 Toyota 4Runner transmission problems start?
Half of the complaints with a recorded mileage happened before about 168,000 miles.
Is it dangerous?
Owners linked 1 crash, 0 fires and 0 injuries to transmission & drivetrain problems on this model year. If you notice symptoms, have the car checked before driving further.
Source: U.S. National Highway Traffic Safety Administration (NHTSA) — owner complaints through October 20, 2026, recalls and defect investigations; fuel economy from the EPA. Complaints are unverified reports and are not proof of a defect. How we rate model years.