This study was conducted to assess the effects of the removal of pesticide residues and microorganisms from yuja (Citrus junos Sieb ex Tanaka) using a surface-washing system, under the following washing conditions: 0.11, 0.42, and 0.73 m/s spray rotation speeds; 0.6, 0.9, and 1.2 MPa water pressure and 0.046, 0.092, and 0.138 m/s conveying speeds. Tap-water treatment was used as the control. The washing efficiency when using squid ink was highly correlated with the conveying speed and the spray rotation speed. In addition, the highest washing efficiency was achieved when the water pressure was 0.9 MPa. The microorganisms were reduced to 0.40 log CFU/g for the tap-water treatment, and all the treatments, except those at the conveying speed of 0.138 m/s and the spray rotation speed of 0.11 rpm (6.07 log CFU/g), produced higher removal efficiencies compared with the tap-water treatment. Reductions of 2.20 and 2.05 log CFU/g were achieved at the spray rotation speeds of 0.42 and 0.73, respectively. The largest reductions were observed when the conveying speed was 0.046 m/s. Higher pesticide residue removal efficiency values were obtained at slower conveying speeds and higher spray rotation speeds. Higher than 50% removal efficiency was achieved when the spray rotation speed was 0.046 m/s for spirodichlofen, deltamethrin, benomyl, thiophanate-methyl, and acequinocyl. Especially, the removal efficiency for benomyl and thiophanate-methyl was more than 90%. It can thus be concluded that the pesticide residues in yuja can be effectively reduced by washing the latter with a less-than-0.092-m/s conveying speed and a higher-than-0.42-m/s spray rotation speed.