Background: Physical exercise habit has some benefits, among others, for physical fitness and cognitive function, as well as preventing incapacitation events caused by low back pain, fatigue, dan cardiovascular diseases. The aim of this study was to find out the description of physical exercise habit among commercial pilot in Indonesia and its affecting factors. Method: This study was conducted with cross sectional design using secondary data from Healthy Lifestyle Survey of Commercial Pilot in Indonesia Year 2016. In this study, data of pilots with CPL and ATPL was analysed. Physical exercise habit was defined appropriately with American College of Sports Medicine (ACSM) recommendation. Data taken were demographic data, job factors, satisfaction of life, body mass index, and waist circumference. Cox regression analysis was used to analyse dominant factors which affect physical exercise habit. Results: Among 644 pilots' data, there were 332 data met the criteria in this study. Proportion of commercial pilots who had appropriate exercise habit was 44%. Dominant factor which affecting exercise habit was age. Compared to pilots aged 20 to 29 years old, pilots aged 50 to 65 years old had 40% less likely to have exercise habit (adjusted relative aisk (RRa) 0.60; 95% Confidence Interval (CI) 0.38 – 0.94; P 0.026). Moreover, flight hours of unplanned flight and overweight were likely to affect physical exercise habit (consecutively aRR 0.58; 95%CI 0.30 – 1.13; P = 0.112 and aRR 0,79; IK95% 0,62 – 1,02; P 0,072). Conclusion: Age group, flight hours of unplanned flight and overweight were likely to affect exercise habit among commercial pilots in Indonesia.