Aims Obesity is known to be associated with an altered thermoregulation as well as a dysregulation of sympathetic nervous system (SNS). Considering the ability of deep transcranial magnetic stimulation (dTMS) to modulate the SNS, we hypothesized a potential role of dTMS in affecting thermoregulation in obesity. Aims of the study were to monitor the effect of a single session of dTMS on body temperature in subjects with obesity, and to correlate the dTMS-induced changes in body temperature with activation of the SNS (epinephrine and norepinephrine release). Methods Twenty-nine subjects with obesity 5 M, 24 F; age 50 (IQR: 58, 38) yrs; BMI 36.1 (IQR: 33.9, 38.7) kg/m 2 were randomized into 2 groups receiving a single session of high frequency stimulation (HF) or sham stimulation. Under neutral thermal conditions, infrared thermography was utilized to assess bilateral fingernail-beds and abdominal temperature. Results During a single session HF, the average temperature of both fingernail-beds decreased. Right-hand temperature difference was statistically greater in HF vs Sham: median = – 1.45 (IQR: – 2.0, – 1.0)  °C for HF, p =  0.009. While temperature variation in the fingernail-bed of left hand was not statistically significant in HF compared to Sham: median = – 1.26 (IQR: – 1.6, –0.5) °C, p =  0.064. Concurrently, when estimating the effect of norepinephrine variation on temperature change of fingernail-bed of left hand, a borderline significant positive association was estimated (beta = 1.09, p =  0.067) in HF. Conclusions Deep TMS revealed to be effective in modulating temperature in subjects with obesity, partially reversing obesity-induced alterations in heat production and dissipation with a potential SNS-mediated mechanism.