Population size and survival are crucial factors to understand population dynamics of a given species, especially those that have long life spans and delayed sexual maturity, such as Pteropodidae bats. We studied the population size and apparent survival of individuals at a day roost site of an endemic cave-dwelling Malagasy fruit bat, Rousettus madagascariensis, in relation with age and sex. 1,801 individuals were captured and tagged over the course of four years in the Grotte des Chauves-souris, Réserve Spéciale d'Ankarana, northern Madagascar. The Cormack-Jolly-Seber model and the POPAN model in the program MARK were used to analyze mark-recapture data and to estimate apparent individual survival and population size. The apparent survival of individuals ranged from 0.46 to 0.60, but exhibited significant variability associated with age, sex, and time. Apparent survival is lower in adults compared to sub-adults (Φ_adult = 0.49; Φ_sub-adult = 0.63). For adults, the apparent survival of males was higher (Φ_male = 0.50; Φ_female = 0.47), and conversely for sub-adults, it was in favor of females (Φ_male = 0.55; Φ_female = 0.70). Population size ranged from 1,245 (CI: 268–3,050) to 5,868 (CI: 3,520–10,601) and was significantly higher during the wet season as compared to the dry season. The survival rate in this population is strongly influenced by mortality and secondarily by dispersal. We found that the apparent survival of individuals has a positive impact on population growth but less than birth rate. Thus, the health and sustainability of the population relies heavily on individual survival.