This work examines the stability of epitaxial 3C-SiC/Si heterojunctions subjected to heat treatments between 1000 °C and 1300 °C. Because of the potential for silicon carbide in high temperature and harsh environment applications, and the economic advantages of growing the 3C-SiC polytype on large diameter silicon wafers, its stability after high temperature processing is an important consideration. Yet recently, this has been thrown into question by claims that the heterojunction suffers catastrophic degradation at temperatures above 1000 °C. Here we present results showing that the heterojunction maintains excellent diode characteristics following heat treatment up to 1100 °C and while some changes were observed between 1100 °C and 1300 °C, diodes maintained their rectifying characteristics, enabling compatibility with a large range of device fabrication. The parameters of as-grown diodes were J0 = 1 × 10-11 A/mm2, n = 1.02, and +/-2V rectification ratio of 9 × 106. Capacitance and thermal current-voltage analysis was used to characterize the excess current leakage mechanism. The change in diode characteristics depends on diode area, with larger areas (1 mm2) having reduced rectification ratio while smaller areas (0.04 mm2) maintained excellent characteristics of J0 = 2 × 10-10 A/mm2, n = 1.28, and +/-2V ratio of 3 × 106. This points to localized defect regions degrading after heat treatment rather than a fundamental issue of the heterojunction.