Background Physical activity (PA) may be a useful tool in the management of menopausal hot flashes (HFs) but findings are generally inconsistent. There are few well-designed and sufficiently powered RCTs. Applying a longitudinal within-person approach offers an alternative way to examine the PA-HFs relationship which enables complete accommodation of inter-individual differences. Objectives Aprospective daily diary study which applied experience sampling methods and time series modeling techniques investigated, at the within-person level, the relationship between objectively measured daily PA of varying intensities and self-reported menopausal HFs. Methods Twenty-four symptomatic middle-aged women (M age=50.4; SD=4.9) completed fitness, body composition and hormonal status screening, and reported on daily HFs using an electronic PDA device across one menstrual cycle or for 30 days (if postmenopausal). Daily PA and PA intensity was measured using accelerometry and subjects completed a battery of psychological measures. Results Within person analysis identified significant relations between PA and HFs in 50% of subjects, although the specific PA indicators that predicted HFs varied, both in terms of direction and magnitude. Perceived control over HFs was the variable that most consistently differentiated between women for whom more PA was associated with fewer HFs as compared to those for whom more PA was associated with more HFs, but other individual difference characteristics such as affect, depressive symptoms, and anxiety were identified. Conclusions There is great individual variation in the way daily PA impacts self-reported HFs. Affective outcomes and perceived control may help potentially explain this variability.