Aim: There is a need to elucidate intermittent Theta burst stimulation (iTBS) as a novel treatment in persistent somatoform pain disorder (PSPD). Methods: Twenty patients were randomly allocated to active iTBS (n = 11) and sham iTBS (n = 9) and received 10 iTBS sessions, 2 sessions per day, sequentially to primary motor and dorsolateral prefrontal cortices for 5 days in a week. Each iTBS session comprised of 2 sec. per train of 10 bursts (3 pulses per burst at 50 Hz; total 30 pulses) and were given with a gap of 5 Hz, total of 20 trains, and 600 pulses. Visual Analogue Scale, Brief Pain Inventory and Global Pain Scale (GPS), Montgomery and Asberg Depression Rating Scale, Hamilton Anxiety Rating Scale - Anxiety, World Health Organization Quality-of-Life Scale-brief, and Pittsburgh Sleep Quality Index were applied at baseline, after last session, and at 2 weeks after last TBS session. Intention to treat analysis was conducted. Results: Both groups were comparable for baseline psychopathology scores including clinical variables like age (t = 0.865; P = 0.398), duration of illness (t = 1.600; P = 0.127), and motor threshold (t = 0.304; P = 0.765). On repeated measures ANOVA, a significant within-group time effect for VAS, BPI-Severity, BPI-Interference, BDI – II, MADRS, HAM-A, and WHOQOL- BREF was found for active and sham TBS groups, respectively. GPS scores had significant within-group (active) * time interaction (F = 11.651; P = .001; ηp2 = 0.538) and between-group * time interaction (F = 3.407; P = 0.044; ηp2 = 0.159). However, between-group * time effect interaction was lost after covariance (F = 1.726; P = 0.196; ηp2 = 0.110). Conclusion: No major adverse effects were reported. Our pilot trial concludes that safe therapeutic efficacy of iTBS in PSPD is inconclusive. Lower total number of sessions along with small sample size may limit the study findings.