This study aimed to compare the clinical features of panic disorder (PD) with comorbid agoraphobia to those of PD alone. We focused on autonomic nervous system (ANS) alterations reflected in heart rate variability (HRV) and executive function deficits reflected in the Stroop test. We retrospectively compared psychometric features, Stroop test results, and resting-state HRV across three groups: a subclinical group with anxiety attack history, a PD group without agoraphobia, and a PD group with agoraphobia. The subclinical group included 10 male and 34 female, the PD without agoraphobia group included 17 male and 19 female, and the PD with agoraphobia group included 11 male and 18 female. The PD with agoraphobia group had higher Symptom Checklist-95 scores than the other groups. Both PD groups had longer reaction times in the Stroop test than the subclinical group. There were no significant differences in HRV parameters between the PD groups with and without agoraphobia. Compared with the subclinical group, the PD with agoraphobia group showed significantly lower values of the natural logarithm of low-frequency HRV. Our results do not support that executive function deficits and ANS alterations are more pronounced with comorbid agoraphobia among PD groups. However, PD with agoraphobia patients showed more complex and severe clinical symptoms in their self-reports. Compared with the subclinical group, PD patients with agoraphobia showed specific features in the natural logarithm of low-frequency HRV. Our findings suggest that agoraphobia comorbidity should be considered when evaluating or treating patients with PD.