Obsessive–compulsive disorder (OCD) is one of the chronic anxiety disorders that interfere with routine individual life, occupational and social functions. There is controversy about the first choice of treatment for OCD between medication and psychotherapy. the aim was to investigate the efficacy of eye movement desensitization and reprocessing (EMDR) compared with medication by citalopram in treatment of OCD. This randomized controlled trial was carried out on 90 OCD patients that randomly were assigned into two groups. They either received therapeutic sessions of EMDR or citalopram during 12 weeks. Both groups blindly were evaluated by the Yale–Brown scale before and after the trial period. Pretreatment average Yale–Brown score of citalopram group was about 25.26 as well as 24.83 in EMDR group. The after treatment scores were 19.06 and 13.6, respectively. There was significant difference between the mean Yale–Brown scores of the two groups after treatment and EMDR was more effective than citalopram in improvement of OCD signs. It is concluded that although both therapeutic methods (EMDR and Citalopram) had significant effect in improving obsessive signs but it seems that in short term EMRD has better effect in improvement of final outcome of OCD.