Jeep · Known Issues

1999 Jeep Wrangler Problems: 12 Known Issues

1999 model year · NHTSA recalls, manufacturer TSBs, and owner forum reports · Updated August 2026

According to Au7o's research across NHTSA recalls, manufacturer TSBs, and owner forum reports, the 1999 Jeep Wrangler has 12 documented known issues, with 5 rated critical. The most serious are In-Tank Fuel Pump Module Failure — Whine, Hard Start & No-Start ($200-$550 repair), Body Tub, Floor Pan & Body-Mount Rust (Torque Box Corrosion) ($400-$3,500 repair), 4.0L Crankshaft Position Sensor Thermal Failure — Random Stalling & Hot No-Start ($60-$250 repair), 4.0L 0331 Cylinder Head Casting Cracking Between #3 and #4 Cylinders ($1,200-$2,600 repair) and Dana 35 Rear Axle Shaft C-Clip Failure ("Grenade") ($300-$2,200 repair). Across all issues with published estimates, repair costs range from $20 to $3,500. DIY maintenance guides at au7o.io.

Frequently Asked Questions

What are the most common Jeep Wrangler problems?

According to Au7o's research across NHTSA recalls, manufacturer TSBs, and owner forum reports, the 1999 Jeep Wrangler has 12 documented issues. The most frequently reported are: In-Tank Fuel Pump Module Failure — Whine, Hard Start & No-Start, Body Tub, Floor Pan & Body-Mount Rust (Torque Box Corrosion), 4.0L Crankshaft Position Sensor Thermal Failure — Random Stalling & Hot No-Start. Of these, 5 are rated critical and should be addressed promptly.

Is the Jeep Wrangler reliable?

The 1999 Jeep Wrangler has 12 known issues compiled from NHTSA recalls, manufacturer TSBs, and owner forum reports. 5 issues are rated critical: In-Tank Fuel Pump Module Failure — Whine, Hard Start & No-Start and Body Tub, Floor Pan & Body-Mount Rust (Torque Box Corrosion) and 4.0L Crankshaft Position Sensor Thermal Failure — Random Stalling & Hot No-Start and 4.0L 0331 Cylinder Head Casting Cracking Between #3 and #4 Cylinders and Dana 35 Rear Axle Shaft C-Clip Failure ("Grenade"). Prospective buyers should inspect for these issues and factor potential repair costs into their purchase decision. Regular maintenance following the manufacturer's schedule helps prevent many common problems.

How much does it cost to fix common Jeep Wrangler problems?

Repair costs for known Jeep Wrangler issues range from $20 to $3,500, depending on the specific problem and whether you choose DIY or professional repair. The most critical issue, In-Tank Fuel Pump Module Failure — Whine, Hard Start & No-Start, typically costs $200-$550 to repair. Au7o provides step-by-step DIY maintenance guides that can help reduce repair costs.

What is the 1997-2006 Jeep Wrangler In-Tank Fuel Pump Module Failure — Whine, Hard Start & No-Start?

The in-tank fuel pump module (pump, sending unit, and level float) wears out on high-mileage TJ Wranglers, producing a loud whine from the tank, hard starting, stalling, and eventual crank-no-start as fuel pressure drops. A top-searched TJ fuel-system failure, sometimes accompani… Repairs typically run $200-$550. Severity: high.

What is the 1994-2006 Jeep Wrangler Body Tub, Floor Pan & Body-Mount Rust (Torque Box Corrosion)?

Distinct from frame corrosion, the steel body tub rusts from the inside out on older Wranglers, especially in salt regions. The spot-welded body-mount channels ('torque boxes') under the floor, the floor-pan seams, and the rocker areas trap moisture and rot around the three body… Repairs typically run $400-$3,500. Severity: high.

What is the 1997-2006 Jeep Wrangler 4.0L Crankshaft Position Sensor Thermal Failure — Random Stalling & Hot No-Start?

The crankshaft position sensor (CPS) on the 4.0L (and 2.5L) inline engines mounts on the transmission bellhousing and is exposed to severe heat soak. As it ages it develops intermittent thermal failure: the engine stalls without warning once hot, then refuses to restart until it… Repairs typically run $60-$250. Severity: high.

What is the 1999-2002 Jeep Wrangler 4.0L 0331 Cylinder Head Casting Cracking Between #3 and #4 Cylinders?

The 4.0L inline-six heads carrying casting number 0331 (used on roughly 1999-2002 builds) were designed with enlarged intake/exhaust ports but left the deck wall between cylinders #3 and #4 too thin. Over high-mileage thermal cycling the head cracks in that area (visible through… Repairs typically run $1,200-$2,600. Severity: high.

What is the 1994-2006 Jeep Wrangler Dana 35 Rear Axle Shaft C-Clip Failure ("Grenade")?

The Dana 35 rear axle fitted to most non-Rubicon YJ/TJ Wranglers uses a C-clip design: each semi-float axle shaft is retained inside the housing only by a C-clip seated in the differential. If a shaft snaps — common with 33-inch-plus tires, a locker, or aggressive trail use — the… Repairs typically run $300-$2,200. Severity: high.

What is the 1997-2006 Jeep Wrangler Heater Core Leak — Coolant Smell & Fogged Windshield?

The heater core inside the dash-mounted HVAC box develops leaks on high-mileage Wranglers, releasing a sweet coolant smell in the cabin, an oily film that fogs the windshield, and eventually a wet passenger-side carpet with unexplained coolant loss. A common older-Jeep HVAC searc… Repairs typically run $400-$900. Severity: medium.

What is the 1997-2006 Jeep Wrangler Throttle Position Sensor (TPS) Failure — Erratic Idle, Stalling & Shift Problems?

The throttle-body-mounted TPS wears and produces an erratic voltage signal, causing high/hunting idle, stalling at stops, hesitation or bucking on acceleration, and — on automatics — erratic or harsh shifting. A very common, high-search TJ driveability complaint that often illumi… Repairs typically run $50-$220. Severity: medium.

What is the 1997-2001 Jeep Wrangler 4.0L Oil Filter Adapter Housing O-Ring Leak?

The 4.0 routes oil through a cast oil-filter adapter housing bolted to the block behind the filter, sealed by a set of rubber O-rings. The O-rings harden and shrink with age/heat, producing a persistent oil leak on the passenger side of the block that runs down the bellhousing an… Repairs typically run $40-$400. Severity: medium.

What is the 1994-2006 Jeep Wrangler 4.0L Two-Piece Rear Main Seal Oil Leak?

A leaking rear main seal is nearly universal on high-mileage 4.0 Wranglers — the two-piece crankshaft seal hardens and weeps oil at the back of the block, dripping onto the bellhousing and often collecting at the transmission. It is one of the most-searched 4.0 oil leaks and is f… Repairs typically run $200-$700. Severity: medium.

What is the 1997-2010 Jeep Wrangler Dana 30 Front Ball Joint Wear — Clunking, Wandering & Steering Vibration?

The solid-axle Dana 30 front end uses pressed-in upper and lower ball joints that wear out on high-mileage Wranglers, especially lifted rigs with larger tires. Worn ball joints introduce play in the steering knuckle, causing clunking over bumps, loose/wandering steering, uneven t… Repairs typically run $200-$700. Severity: medium.

What is the 1994-2006 Jeep Wrangler 4.0L Valve Cover Gasket Oil Leak?

One of the most common 4.0 oil leaks: the valve cover gasket hardens and seeps, typically worst at the rear of the head, leaving oil and grime down the back of the block and sometimes dripping onto the exhaust (burning-oil smell). Frequently mistaken for a more serious rear main… Repairs typically run $30-$300. Severity: low.

What is the 1994-2006 Jeep Wrangler NP231 Transfer Case Rear Output Shaft Seal / Slip-Yoke Leak?

The NP231 (Command-Trac) transfer case in YJ/TJ Wranglers uses a slip-yoke rear output. The rear output shaft seal is a chronic leak point — the exposed slip yoke picks up grit and rust that scores the seal, and a worn tail-housing bushing lets the yoke move and tear the seal. Re… Repairs typically run $20-$400. Severity: low.

All 12 Known Issues

1997-2006 Jeep Wrangler: 4.0L Crankshaft Position Sensor Thermal Failure — Random Stalling & Hot No-Start#

1999-2002 Jeep Wrangler: 4.0L 0331 Cylinder Head Casting Cracking Between #3 and #4 Cylinders#

1997-2001 Jeep Wrangler: 4.0L Oil Filter Adapter Housing O-Ring Leak#

1994-2006 Jeep Wrangler: 4.0L Two-Piece Rear Main Seal Oil Leak#

1994-2006 Jeep Wrangler: 4.0L Valve Cover Gasket Oil Leak#

1997-2006 Jeep Wrangler: In-Tank Fuel Pump Module Failure — Whine, Hard Start & No-Start#

1997-2006 Jeep Wrangler: Throttle Position Sensor (TPS) Failure — Erratic Idle, Stalling & Shift Problems#

1994-2006 Jeep Wrangler: Dana 35 Rear Axle Shaft C-Clip Failure ("Grenade")#

1994-2006 Jeep Wrangler: NP231 Transfer Case Rear Output Shaft Seal / Slip-Yoke Leak#

1994-2006 Jeep Wrangler: Body Tub, Floor Pan & Body-Mount Rust (Torque Box Corrosion)#

1997-2006 Jeep Wrangler: Heater Core Leak — Coolant Smell & Fogged Windshield#

1997-2010 Jeep Wrangler: Dana 30 Front Ball Joint Wear — Clunking, Wandering & Steering Vibration#

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