We studied variation in the Body Condition Index (BCI) of a Malagasy frugivorous bat, Rousettus madagascariensis (Pteropodidae), in relation to the abundance of ectoparasite flies, Eucampsipoda madagascarensis (Nycteribiidae). The study site was a cave in northern Madagascar that was visited three times during the dry season (September 2014, 2015, and 2016) and two times during the wet season (January 2015 and 2016). Two measurements were taken from all captured Rousettus to evaluate their BCI: forearm length and body mass. In total, we sampled ectoparasites from 1,030 R. madagascariensis during the five visits. The BCI of sampled bats showed statistical differences when compared by season and segregated by different age and sex classes, with generally the higher mean values during the wet season and lower values during the dry season. In most cases, the abundance of E. madagascarensis for each of the different bat age and sex classes did not differ between seasons. A weak positive relationship was found for most seasonal visits between host BCI and nycteribiid abundance, specifically in adult males, and sub-adult males and females; such a relationship was not observed for neonates. On the basis of a GLM analysis, our results support the hypothesis of a positive relationship between ectoparasite abundance and host BCI. The seasonal variation in host BCI was not related to nycteribiid abundance, but rather some other factor associated with host physical condition, such as the availability of fruit and correlated shifts in body mass.