The star formation rate (SFR) is a fundamental parameter for describing galaxies and inferring their evolutionary course. H ii regions yield the best measure of instantaneous SFR in galaxies, although the derived SFR can have large uncertainties depending on tracers and assumptions. We present an SFR calibration for the entire molecular gas disk of the nearby Seyfert galaxy NGC 1068, based on our new high-sensitivity Atacama Large Millimeter/submillimeter Array 100 GHz continuum data at 55 pc (= 0.″8) resolution in combination with the Hubble Space Telescope Paα line data. In this calibration, we account for the spatial variations of dust extinction, electron temperature of H ii regions, AGN contamination, and diffuse ionized gas (DIG) based on publicly available multiwavelength data. Especially, given the extended nature and the possible nonnegligible contribution to the total SFR, a careful consideration of DIG is essential. With a cross-calibration between two corrected ionized gas tracers (free–free continuum and Paα), the total SFR of the NGC 1068 disk is estimated to be 3.2 ± 0.5 M ⊙ yr−1, one-third of the SFR without accounting for DIG (9.1 ± 1.4 M ⊙ yr−1). We confirmed a high SFR around the southern bar end and the corotation radius, which is consistent with the previous SFR measurements. In addition, our total SFR exceeds the total SFR based on 8 μm dust emission by a factor of 1.5. We attribute this discrepancy to the differences in the young stars at different stages of evolution traced by each tracer and their respective timescales. This study provides an example to address the various uncertainties in conventional SFR measurements and their potential to lead to significant SFR miscalculations.