Introduction: Respiratory sinus arrhythmia (RSA) may be a psychophysiological measure that can gauge change processes in psychotherapy. RSA is a cardiovascular marker of nervous system functioning and has been proposed as an index of social engagement. Given the emphasis on social relationships in Functional Analytic Psychotherapy (FAP), RSA may be useful for understanding the process of change in FAP. The current study details the logic of using RSA as a measurement tool and provides data to establish proof of concept. Methods: RSA data were collected from three participants in a multiple baseline experiment which involved a control condition of reading two-person plays and a FAP condition. Sessions were coded using the FAP Rating Scale. RSA was calculated for each session and each client-therapist interaction. Results: RSA higher during FAP sessions (P1Mean = 6.60, P2Mean = 6.41, P3Mean = 6.32) than the control condition (P1Mean = 6.29, P2Mean = 5.79, P3Mean = 5.96). Conclusions: Data are consistent with outcomes that might be anticipated during therapy and suggest RSA could improve as a function of treatment. RSA was able to be isolated for therapeutic moves when coded at the turn-by-turn level. Thus, data suggest RSA’s utility for measuring therapy processes and outcomes.