ABSTRACT Objectives This study examined therapist–client physiological synchronisation, indexed by heart rate variability (HRV), in meditation versus emotionally supportive sessions (control condition) and its association with clients' affective evaluations. Methods This was a randomised experimental study. Participants were assigned to a meditation session ( n = 20) or an emotional support session ( n = 20). HRV was assessed at baseline and post‐session; an additional mid‐session HRV assessment was obtained in the meditation condition immediately following the meditation segment. Clients reported positive and negative affect and evaluated the session. Results No significant therapist–client HRV correlations were observed at baseline or at the end of the session in either condition. However, in the meditation condition, changes in therapists' HRV from baseline to mid‐session and from baseline to post‐session were associated with clients' affective evaluations, whereas no such associations emerged in the control condition. Finally, a factor analysis revealed two non‐coherent factors of therapists' and clients' HRV before and after the session in controls, and a single factor including all HRV measures of therapists and clients in the meditation condition. Conclusions Therapist autonomic regulation during meditation may relate to clients' immediate emotional experience. Further research using longitudinal and dynamic designs is needed to clarify mechanisms of physiological synchronisation in psychotherapy.