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Background Postural tachycardia syndrome (POTS), a subset of orthostatic dysregulation, has been reported to be associated with anxiety. POTS can be classified into two forms based on the degree of tachycardia during orthostasis. Reportedly, POTS with decreased orthostatic heart rate increase is associated with suppressed cardiac parasympathetic activity and increased sympathetic activity in the supine position. In this study, the relationship between the two types of POTS and anxiety was evaluated in terms of autonomic function. Methods Fifty-two patients (23 males, aged 10–15 years) who were diagnosed with POTS at the Department of Pediatrics, Osaka Medical and Pharmaceutical University from 2019 to 2021, provided completed the State-Trait Anxiety Scale for Children (STAIC) questionnaire. They then completed a standing test and were accordingly classified into the two groups of POTS, the Su group, with tachycardia from the supine position and a low heart rate increase on standing, and the SI group, with a high heart rate increase during standing. Autonomic function was assessed by frequency analysis (MemCalc method) based on heart rate, blood pressure changes, heart rate, and blood pressure variability during the orthostatic test. Results Patients in the Su group had higher characteristic anxiety, lower cardiac parasympathetic activity (RR-HF) in the supine position, and greater variability in cardiac parasympathetic activity during orthostasis than those of patients in the SI group. The Su group had a greater decrease in cardiac index on standing than that of the SI group. Conclusions The Su group results may be partly attributed to chronically low venous return. We also found that patients in the Su group had low parasympathetic activity in the supine position, which may interact with the anxiety-prone characteristics of these patients. Therefore, it seems necessary to consider both physical and psychosomatic treatment approaches for patients with POTS. Trial registration The clinical trial registry of Osaka Medical and Pharmaceutical University, Clinical Trial Registration No. 2662-2. Registered 5 March 2019. https://ompu.bvits.com/rinri/Common/print_approve.aspx?ID=3479