Purpose: A tractor is a versatile machine and is used in many applications other than agriculture, like in mining, transportation, and construction. One such application is with front end loader where it requires a frequent change in direction of motion. To meet this requirement a power shuttle transmission system is used in agricultural tractors. The present research focuses on the transmission control algorithm development for one such a power shuttle transmission system. Methods: The development and testing of the control algorithm were carried out in MATLAB & Simulink environments with an additional specific strategy for the clutch pressure modulation. Further National Instruments CompactRIO (NI-cRIO) was used to verify the system’s functionality in a real-time environment. Results: The obtained simulation results were in close accordance with the real system in terms of system functionality and response time. The alikeness between the simulated and actual response time varies from − 20 to 11% and the tractor intended functionality is verified as per the developed control logic. Conclusion: This research provides an approach for the development of control strategies for tractor transmission systems and their rapid prototype development and testing.