Abstract The work in this paper builds upon the relatively well-studied seasonal cycle of the Indian Ocean heat transport by investigating its interannual variability over a 41-yr period (1958–98). An intermediate, two-and-a-half-layer thermodynamically active ocean model with mixed layer physics is used in the investigation. The results of the study reveal that the Indian Ocean heat transport possesses strong variability at all time scales from intraseasonal (10–90 days) to interannual (more than one year). The seasonal cycle dominates the variability at all latitudes, the amplitude of the intraseasonal variability is similar to the seasonal cycle, and the amplitude of the interannual variability is about one-tenth of the seasonal cycle. Spectral analysis shows that a significant broadband biennial component in the interannual variability exists with considerable coherence in sign across the equator. While the mean annual heat transport shows a strong maximum between 10° and 20°S, interannual variability is relatively uniform over a broad latitudinal domain between 15°N and 10°S. The heat transport variability at all time scales is well explained by the Ekman heat transport, with especially good correlations at the intraseasonal time scales. The addition of the Indonesian Throughflow does not significantly affect the heat transport variability in the northern part of the ocean.