The present paper deals with the performance analysis of gas turbines with online pulse jet system for air filter cleaning. In order to evaluate the engine performance before, during and after the cleaning procedure, a mathematical model of GE MS6001FA gas turbine has been implemented using GateCycle software. The model was calibrated and tested using real engine monitoring data. A comparison of the engine behavior from the model and experimental data shows that the results can be calculated with errors below 2% for the input conditions simulated in the present study. The GateCycle model was used to evaluate engine performance before, during and after engine pulse jet activation. On the basis of the results it is possible to state that air filter cleaning slightly increase engine performance in normal industrial environment.