A system and a method of controlling a transmission for a vehicle can protect the transmission by controlling an oil temperature in the transmission when driving on a long uphill road. The system may include: an engine generating driving torque; a transmission converting and outputting the driving torque generated at the engine; a lock-up clutch disposed between the engine and the transmission, and directly coupling the engine to the transmission selectively; a data detector detecting data for controlling the transmission; and a controller determining whether a long uphill road condition is satisfied based on the data, determining whether a protective logic operating condition is satisfied if the long uphill road condition is satisfied, and operating a protective logic if the protective logic operating condition is satisfied.