A system includes a two stage heat exchanger and a processor. The processor is configured to receive a call from a thermostat and execute, in response to the call, an adaptive staging algorithm. The adaptive staging algorithm is configured to determine, in response to a recent cycle of the two stage heat exchanger being a first stage cycle, a first stage up time of the two stage heat exchanger as a first function of a first value, the first value corresponding to the recent cycle being the first stage cycle. The adaptive staging algorithm is also configured to determine, in response to the recent cycle of the two stage heat exchanger being a second stage cycle, a second stage up time of the two stage heat exchanger as a second function of a second value, the second value corresponding to the recent cycle being the second stage cycle, where the first and second values are different.