The goal of this study was to explore why certain patients in a previous study on exposure therapy for flight phobia did not experience an improvement in their conditions. Participants from a treatment study (N = 45) were selected according to post-treatment results and divided into two groups: the unsatisfactory treatment outcome group (UTO, N = 10) and the satisfactory treatment outcome group (STO, N = 10). The differences between these two groups prior to receiving exposure therapy were analyzed at the behavioral, physiological, and cognitive levels. The UTO participants had been avoiding flying longer than the STO phobics. Following Thayer and Lane’s neurovisceral model of emotion regulation, heart rate variability was analyzed at two levels: tonic and phasic. Low frequency and high frequency (HF) power were calculated in the frequency domain and Sample Entropy was computed in the time domain. The tonic HF power of the UTO group was higher than the STO group’s tonic HF power. In the phasic level, while the STO group’s HF power decreased under exposure and subsequently returned to baseline level, the UTO group demonstrated a more rigid pattern. Finally, the STO group reported higher emotional involvement than the UTO group when they were shown a sample of the therapy. Based on these results, the challenge of matching exposure therapy to each patient’s profile is discussed.