The exploration of Theta Burst Stimulation (TBS) in Obsessive-compulsive disorder (OCD) treatment is still in its nascent stages, and these initial findings underscore the need for further research to optimize stimulation parameters and identify patient subgroups that may benefit the most from this intervention. The current paper aims to contribute to this growing body of literature by presenting original randomized controlled trial research on the efficacy of Intermittent and Continuous TBS as add-on interventions in treatment-resistant OCD. The study was conducted between December 2019 and December 2022 in a randomized, double-blind, sham-controlled design. The participants with severe OCD (n = 27) were randomly allocated into active stimulation (iTBS and cTBS, n = 14) and sham stimulation (n = 13) groups and observed for a follow-up period of 3 months. Depressive symptoms and general functioning were also monitored. Despite growing scientific evidence supporting the efficacy of repetitive Transcranial Magnetic Stimulation (rTMS) and TBS in treating OCD, our study yielded inconclusive results. The heterogeneity of symptom presentations in our study group complicates the assessment of treatment efficacy. While significant improvements were observed across several measures over time, many effects were independent of the specific intervention group. Subgroup analysis and follow-up results suggest that TMS, particularly cTBS, may offer some benefit in managing OCD symptoms, although larger sample sizes and more focused studies are needed to confirm these findings.