Background: Whether whole-body energy balance is associated with perceived stress in young adults is unclear. Aim: To examine associations of estimated free-living energy balance with physical and psychological stress during 28-day monitoring. Methods: This secondary analysis of an observational study included 18 Japanese male university students with at least 14 valid accelerometer days (at least 600 min/day). Energy intake was estimated using the Brief-type Self-administered Diet History Questionnaire; total energy expenditure was estimated from accelerometry plus resting metabolic rate. Physical and psychological stress were assessed before and after monitoring using 100-mm visual analog scales. Baseline-adjusted linear regression was used. Summary: Mean energy balance was -79 kcal/day (SD 531). Energy balance was not clearly associated with post-monitoring physical stress (B = 0.067 per 100 kcal/day, 95% CI -1.604 to 1.737; p = 0.933) or psychological stress (B = 0.314, 95% CI -2.571 to 3.199; p = 0.820). No clear association between estimated free-living energy balance and post-monitoring stress was detected.