OBJECTIVE To investigate whether keratoconus (KC) patients who applied the corneal collagen cross-linking (CXL) and two different contact lens (CL) showed any differences in complaints and findings following the CXL. METHODS This prospective, comparative, double-blind clinical study involved 60 eyes of 60 patients (38 female and 22 male). At the end of the CXL procedure, CL (Balafilcon A) was inserted in 29 patients (Group-1) while CL with different material content (Hioxifilcon A) designed for therapeutic/bandage purposes were inserted in 31 patients (Group-2). RESULTS On the 1st and 3th day after the CXL, there were no statistically significant differences between the groups in terms of the postoperative symptoms. On the 3th day after the CXL, all cases of both two groups were found to complete the corneal re-epithelialization. There was more PE ratio in the patients who had allergic conjunctivitis. CONCLUSIONS With the use of Balafilcon A and Hioxifilcon A lens materials, KC patients who underwent the CXL were found to have similar symptoms and clinical findings after the CXL. However, epithelial staining and PE were observed more in KC cases accompanied by allergic conjunctivitis.