A seedling picking device is an essential component for an automatic transplanter to automatically convey the seedling to the dibbling part. It is necessary to find the appropriate material and dimensions for the picking device gears to avoid mechanical damage and increase their durability. Therefore, the objectives of this research were to analyze the stress of a picking device gear mechanism in order to select suitable materials and dimensions, and to predict the fatigue life by considering the damage level. The picking device gear shaft divided the input power into two categories, i.e., crank and cam gear sets. Finite element analysis simulation and American Gear Manufacturers Association standard stress analysis theory tests were conducted on both of the crank and cam gear sets for different materials and dimensions. A test bench was fabricated to collect the load (torque) data at different gear operating speeds. The torque data were analyzed using the load duration distribution method to observe the cyclic load patterns. The Palmgren–Miner cumulative damage rule was used to determine the damage level of the picking mechanism gears with respect to the operating speed. The desired lifespan of the transplanter was 255 h to meet the real field service life requirement. Predicted fatigue life range of the picking mechanism gears was recorded as from 436.65 to 4635.97 h, making it higher (by approximately 2 to 18 times) than the lifespan of the transplanter. According to the analyses, the “Steel Composite Material 420H carbon steel” material with a 5 mm face width gear was suitable to operate the picking device for a 10-year transplanter service life. The analysis of stress and fatigue presented in this study will guide the design of picking device gears with effective material properties to maintain the recommended service life of the pepper transplanter.