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In the present study, we examined metabolic, morphological and neurochemical changes in male striped hamsters (Cricetulus barabensis) in response to variations in food availability. Males with low and high levels of metabolic rate (MR: L-MR and H-MR, respectively), defined by their activity MR, were compared. In Experiment 1, 36-h food deprivation was found to significantly decrease MR levels, body fat content, mass of small and large intestines, and leptin gene expression in the white adipose tissues in male hamsters. Interestingly, L-MR males displayed decreased MR during both the day and night phases of circadian cycles, whereas H-MR males only showed a decrease in MR during the day (resting phase). These data indicate that individual differences in physical activity were associated with animals’ different metabolic responses to food deprivation. In Experiment 2, both groups of males went through a 4-week fasting and re-feeding (re) paradigm. H-re males showed a persistent high level of MR, with decreased body fat content and a trending decrease in leptin mRNA expression, compared to L-re males. Together, our data indicate that male striped hamsters with different levels of physical activity display altered, adaptive changes in response to variations in food availability. The neurochemical involvement of such adaptive changes needs to be further studied.