The purpose of this study was to quantitatively analyze heart rate variability (HRV) in patients with central serous chorioretinopathy (CSC) by using a smartphone-based application (ANBAI: DUMSCO Inc.) for measurement, and to clarify its relationships with CSC. The subjects were 64 CSC patients (mean age 48.7 +/- 7.6 years, 57 males and 7 females). After providing consent, the patients downloaded ANBAI apps to their smartphones. HRV was measured by photoelectric volume pulse wave measurement with a smartphone camera each morning for a minimum of 1 week. The primary outcome was to analyze HRV by calculating log LF/HF (Low Frequency/High Frequency components), an index of autonomic tone, which was then compared with a control group of 35,226 individuals from the application. Secondary outcome measures included disease duration, body mass index, exercise habits, smoking history, steroid use, occupation, lifestyle regularity, psychological fatigue, physical fatigue, and average sleep time. The log LF/HF was significantly higher in the patient group than in the control group (P < 0.001). Log LF/HF was significantly lower in patients with exercise habits as a factor contributing to log LF/HF in the patient group (P = 0.019). Analysis of HRV in CSC patients showed an impairment of the autonomic nervous system. Exercise habits may also be associated with CSC.