As interest in eco-friendly work vehicles grows, research on the powertrains of eco-friendly tractors has increased, including research on the development of eco-friendly vehicles (tractors) using hydrogen fuel cell power packs and batteries. However, batteries require a long time to charge and have a short operating time due to their low energy efficiency compared with hydrogen fuel cell power packs. Therefore, recent studies have focused on the development of tractors using hydrogen fuel cell power packs; however, there is a lack of research on powertrain performance analysis considering actual working conditions. To evaluate vehicle performance, an actual load measurement during agricultural operation must be conducted. The objective of this study was to conduct an efficiency analysis of powertrains according to their power source using data measured during agricultural operations. A performance evaluation with respect to efficiency was performed through comparison and an analysis with internal combustion engine tractors of the same level. The specifications of the transmission for hydrogen fuel cell and engine tractors were used in this study. The power loss and efficiency of the transmission were calculated using ISO 14179-1 equations, as shown below. Plow tillage and rotary tillage operations were conducted for data measurement. The measurement system consists of four components. The engine data load measurement was calculated using the vehicle’s controller area network (CAN) data, the axle load was measured using an axle torque meter and proximity sensors, and fuel consumption was measured using the sensor installed on the fuel line. The calculated capacities, considering the engine’s fuel efficiency for plow and rotary tillage operations, were 131.2 and 175.1 kWh, respectively. The capacity of the required power, considering the powertrain’s efficiency for hydrogen fuel cell tractors with respect to plow and rotary tillage operations, was calculated using the efficiency of the motor, inverter, and power pack, and 51.3 and 62.9 kWh were the values obtained, respectively. Considering these factors, the engine exhibited an efficiency of about 47.9% compared with the power pack in the case of plow tillage operations, and the engine exhibited an efficiency of about 29.3% in the case of rotary tillage operations. A hydrogen fuel cell tractor is considered suitable for high-efficiency and eco-friendly vehicles because it can operate on eco-friendly power sources while providing the advantages of a motor.