The 5S-FE was available in several variations each being distinguished by valve cover design. The first generation, introduced in the 1990–92 Celica GT/GT-S and MR2, had a power rating of 130 hp and 144 lbs-ft/torque. The second generation was introduced in 1993 with the fifth generation (ST184) Celica, and continued through the sixth generation (ST204) Celica. The second generation was also used in the MR2 (SW21) and Camry/Scepter (XV10) series and had a power output of 135 hp and 145 lbs-ft/torque. It had slightly less aggressive cams, no cold start injector, a knock sensor, and more aggressive tuning to give it slightly more power. In states that had adopted California emission standards the 5S-FE was rated at 130 hp and 145 lbs-ft/torque due mainly to emission equipment used to meet those emission regulations. The third generation was the last 5S-FE engine produced and was used in the 1997–01 Camry XV20 and 1999–01 Camry Solara; however, from 1996 onward, the engine received a crank angle sensor instead of a cam angle sensor for a smoother idle. From 1997 to 1999 the engine produced 133 hp at 5,200 rpm and 147 lbs-ft/torque at 4,400 rpm. From 2000 to 2001, the engine received modest improvements to increase power output to 136 hp at 5,200 rpm and 150 lbs-ft/torque at 4,400 rpm. The 5S-FE was replaced in all applications by the 2.4 L 2AZ-FE.

California specification 1994-1996 5S-FEs in the Celica and Camry used air-assisted, 250 cc injectors, and sequential fuel injection for reduced emissions over the grouped (2+2) firing scheme. The 1994-1995 MR2 did not receive this change, nor did Camrys/Celicas in federal emissions states.

Camry 5S-FEs have a counter-rotating balance shaft assembly to reduce noise, vibration, and harshness. They reduce the 2nd order vibrations common to 4-cylinder engines by spinning at double the crankshaft speed. The 1994-1999 Celica and 1991-1995 MR2 5S-FEs lack these balance shafts, so any 5S-FE engine with balance shafts likely came from a Camry.

In 1997, for the fourth generation Camry, the 5S-FE was updated for the last time. This engine received a direct ignition system with external camshaft and crankshaft sensors. This system used a waste-spark design, and the coils had integrated igniters. The engine did not use a typical coil-on-plug design, but rather two coil+igniter assemblies mounted near cylinder four, and provided spark via normal high-tension cords (spark plug wires). This change means that the 1997-01 Camry 5S-FE has a blocked off distributor mounting hole and could be used with older 5S-FEs without swapping cylinder heads.

The 1997-99 Camry 5S-FE continued with the air-assisted, 250 cc injectors. The Camry 5S-FE also had a factory 4-to-1 exhaust design - in Federal form, it had no pre-catalyst, although the California version did replace the collector design of the Federal version with a warm-up pre-catalyst for reduced cold start emissions.

For 2000 Toyota removed the air-assisted injectors and moved to superfine atomization (~50 micrometers), 12-hole, 235 cc injectors made by Denso. They are of a different design, and required a change in the cylinder head casting.

For 2001 Toyota started fitting factory MLS (multi-layer steel) head gaskets and other metal gaskets layered with Viton to engines, including the 5S-FE. MLS head gaskets require cylinder head and cylinder block resurfacing on older engines to ensure proper sealing; consequently, the MLS head gasket did not supersede the old composite head gasket.

The 1994-99 Celica 5S-FE was not updated with these changes, and continued to use a distributor and the older electronic control system and injectors. Any used engine marked as a 1997-01 Camry 5S-FE with a distributor is a Celica 5S-FE or older Camry 5S-FE.