The sodium-calcium exchanger isoform 1 (NCX1) operating in calcium-efflux mode plays an important role in maintaining calcium homeostasis in the heart. Paradoxically, activity of NCX1 in calcium-influx mode contributes to the pathological intracellular calcium overload during cardiac ischemia-reperfusion injury. Reactive oxygen species (ROS) also contribute to myocardial dysfunction in ischemia-reperfusion and are reported to alter NCX1 activity. However, the molecular mechanism(s) by which ROS modifies NCX1 activity have not been elucidated. Therefore, the effects of the ROS, H2O2, on recombinant NCX1 splice variants were studied using the patch-clamp technique. H2O2 irreversibly increased calcium-influx mode activity in the cardiac NCX1.1 splice variant, without affecting calcium-efflux mode activity. In direct contrast, H2O2 inhibited the calcium-influx mode of the vascular NCX1.3 splice variant indicating that these disparate effects of H2O2 may be dependent on the exon complement of the alternative splicing region. Using NCX1 splice variants with various exon compositions, the mutually exclusive exons A and B were found to bestow the differential effects of H2O2 on NCX1 function. As NCX1 inhibition is a potential therapeutic strategy for ischemia-reperfusion injury, the effects of the NCX1 inhibitor KB-R7943 were examined. KB-R7943 was approximately 7-fold less potent at inhibiting NCX1 activity after H2O2 modification. In summary, this study provides insights into the molecular regulation of NCX1 by ROS and indicates that ROS may elicit differential effects in various tissues depending on the exon composition of the splice variant expressed. These results also highlight that the potency of NCX1 inhibitors may be impaired under conditions of oxidative stress.