This study compared the electromyographic activities and input performance of computer operators using a computer mouse and a trackball. Muscle activities were assessed at the upper trapezius (UT), middle deltoid (MD), extensor digitorum (ED), and first dorsal interosseous muscle (FDI). Twenty-six healthy subjects were recruited, and the test order was selected randomly for each subject. The task set was to click moving targets on a Windows program. The EMG amplitude was normalized using the percentage of reference voluntary contraction for UT and MD and the percentage of maximal voluntary contraction for ED and FDI. To analyze the differences in EMG activity, a paired t-test was used. UT muscle activities were significantly greater when the computer mouse was used (p<.05). FDI muscle activities were significantly greater when the trackball was used (p<.05). Using a trackball can reduce the load on the UT during computer work and help to prevent and manage work-related musculoskeletal disorders.