Long term cognitive studies in humans and nonhuman primates such as macaques are difficult because of their long lifespan. The common marmoset (Callithrix jacchus) is a non-human primate who shares with humans many features characteristic of primates, including a complex brain and cognitive function. They also have a short lifespan (~10 years) that makes them a great model in studies of cognitive aging. This study focuses on the rate of decline in cognitive function in male and female marmosets based on performance on reversal learning tasks over 2 years of testing. We found that marmosets improved their overall performance from Year 1 to Year 2 due to practice effect, but that females exhibited an impairment in reversal learning compared to males in both years. We also found important individual differences, with some monkeys showing decline in Year 2 compared to Year 1 while most monkeys maintained or improved their performance in reversal learning over the two years. We conclude that (1) cognitive flexibility, as assessed by reversal learning, is impaired in middle-aged female marmosets compared to males, likely due to sex differences in habitual vs. goal-directed behavior, and (2) that reversal learning is a sensitive measure that can capture one year individual changes in cognitive function.