Accumulating evidence suggests that the magnetic resonance imaging (MRI) scanner can act as a stressor, eliciting subjective and neuroendocrine stress responses. Approaches to familiarize subjects with the scanner could help minimizing unintended effects on neural activation patterns of interest. Controlled studies on the effects of a scanner training are however missing. Using a comparative design, we analyzed within- and between session changes in subjective and neuroendocrine stress parameters in 63 healthy, scanner-naïve adults who participated in a two-day training protocol in an MRI, mock, or lab environment. A habituation task was used to assess within-session changes in subjective and neuroendocrine (cortisol) stress parameters; between-session changes were indicated by differences between days. MRI and mock, but not lab training were successful in reducing subjective distress towards the scanner. In contrast, cortisol reactivity towards the training environment generally increased during day 2, and the percentage of cortisol responders particularly rose in the mock and MRI groups. Within-session habituation of subjective arousal and anxiety was observed during both days and irrespective of training condition. Present findings demonstrate that training in a scanner environment successfully reduces subjective distress, but may also induce sensitization of endocrine stress levels during repeated scanning. Subjective distress can further be stabilized by acclimating subjects to the environment prior to the MRI assessment, including a short habituation phase into the assessment protocol. If replicated, present findings should be considered by researchers employing repeated measurement designs where subjects are exposed to a scanner more than once.