Calcium is a key ion and is known to mediate signalling pathways between cytosol and mitochondria and modulate mitochondrial energy metabolism. To gain a quantitative, biophysical understanding of mitochondrial Ca2+ regulation, we developed a thermodynamically balanced model of mitochondrial Ca2+ handling and bioenergetics by integrating kinetic models of mitochondrial Ca2+ uniporter (CU), Na+–Ca2+ exchanger (NCE), and Na+–H+ exchanger (NHE) into an existing computational model of mitochondrial oxidative phosphorylation. Kinetic flux expressions for the CU, NCE and NHE were developed and individually parameterized based on independent data sets on flux rates measured in purified mitochondria. While available data support a wide range of possible values for the overall activity of the CU in cardiac and liver mitochondria, even at the highest estimated values, the Ca2+ current through the CU does not have a significant effect on mitochondrial membrane potential. This integrated model was then used to analyse additional data on the dynamics and steady-states of mitochondrial Ca2+ governed by mitochondrial CU and NCE. Our analysis of the data on the time course of matrix free [Ca2+] in respiring mitochondria purified from rabbit heart with addition of different levels of Na+ to the external buffer medium (with the CU blocked) with two separate models – one with a 2: 1 stoichiometry and the other with a 3: 1 stoichiometry for the NCE – supports the hypothesis that the NCE is electrogenic with a stoichiometry of 3: 1. This hypothesis was further tested by simulating an additional independent data set on the steady-state variations of matrix free [Ca2+] with respect to the variations in external free [Ca2+] in purified respiring mitochondria from rat heart to show that only the 3: 1 stoichiometry model predictions are consistent with the data. Based on these analyses, it is concluded that the mitochondrial NCE is electrogenic with a stoichiometry of 3: 1.