In behavioural and neurophysiological pain studies, multiple types of calibration methods are used to quantify the individual pain stimuli. Often studies lack calibration procedure implementation, have a vague protocol description, do not provide quality quantification, and omit required control for gender pain differences, hampering study repetition and interexperimental comparisons. Moreover, typical calibration procedures require a high number of stimulations which may cause participants’ discomfort and stimuli habituation. To overcome those shortcomings, we present an automatic calibration procedure with a novel stimuli estimation method for intra epidermal stimulation adjusted to the magnetoencephalography environment. We provide an in-depth data analysis of the collected self-reports from seventy healthy volunteers (37 males) and propose a method based on a dynamic truncated linear regression model (tLRM). We compare its estimates for the sensation (t), and pain (T) thresholds, as well as for the mid-pain stimulation (MP), with those calculated using a traditional estimation method and standard linear regression models. Compared to the other methods, tLRM exhibits higher R2 and requires 36% fewer stimuli application and has significantly higher t and lower T and MP intensities. Regarding sex differences, t and T were found to be lower for females compared to males, regardless of the estimation method. The proposed tLRM method quantifies the calibration procedure quality, minimizes its duration and invasiveness, as well as provides validation of linearity between stimuli intensity and subjective scores, making it an enabling technique for further studies. Moreover, our results highlight the importance of control for gender in pain studies