A transmission system is disclosed for use with an engine. The transmission system may have a plurality of gear sets, an input member configured to be powered by the engine and to drive the plurality of gear sets, an output member driven by the plurality of gear sets, and at least one clutch configured to selectively engage select gears of the plurality of gear sets. The transmission system may also have a controller in communication with the engine. The controller may be configured to generate an estimated temperature of the at least one clutch. The controller may further be configured to selectively derate the engine based on the estimated temperature.