To prevent infections associated with biomedical catheters, various antimicrobial coatings have been investigated. However, those materials do not provide consistent antibacterial effects or biocompatibility, generally, due to degradation of the coating materials, in vivo. Additionally, biomedical catheters must have low surface friction to reduce tribological damage. In this study, we developed an antifouling surface composed of biocompatible amino acids (leucine, taurine, and aspartic acid) on polyimide, via modification using a series of facile immersion steps with waterborne reactions. The naturally derived amino acid could be formed highly biostable amide bonds on the polyimide surface like peptides. The amino acid-modified surface formed a water layer with antifouling performance through the hydrophilic properties of amino acids. Amino acid-mediated modification reduced adhesion up to 84.45% and 94.81% against Escherichia coli and Staphylococcus epidermidis, respectively, and exhibited an excellent prevention to adhesion against the proteins, albumin and fibrinogen. Evaluation of the surface friction of the catheter revealed a dramatic reduction in the tribological force after amino acid modification on polyimide that of 0.81 N to aspartic acid of 0.44 N. These results clearly demonstrate a reduced occurrence of infections, thrombi and tribological damage following the relatively facile surface modification of catheters. The proposed modification method can be used in a continuous manufacturing process via using the same time of modification steps for the easy producing the product. Moreover, the method uses biocompatible naturally derived materials and can be applied to medical equipment that requires biocompatibility and biofunctionality with polyimide surfaces.