This study evaluated effect of alternating electric field on pectinesterase activity in 5-mL Navel orange juice samples subject to ohmic pasteurization. An empirical Weibull kinetic model for enzyme inactivation was fitted to data from conventional and ohmic heating runs. Discretization of time-dependent inactivation rates allowed accounting for a nonisothermal process, with similar equivalent times between paired runs indicating comparable time-temperature profiles across heating methods. Conditions were 60 Hz, 32–36 V/cm, holding temperatures 60–90 °C, holding times 0–200 s in a custom cell with stirring, and two Ti-Pt electrodes. Residual pectinesterase activity was assayed with a traditional titration method at pH 7.5 and 30 °C. The stochastic Monte Carlo resampling method of smoothed bootstrap estimated the parameter populations to propagate experimental uncertainty on enzyme activity. Joint parameter populations and confidence regions agree with least squares estimates, and indicate that kinetic parameters depend on heating technology. This difference is evidence of electric field effects on pectinesterase activity, which is more evident at lower heat process intensities; however, the thermal denaturation seems to overcome other effects at higher processing times and temperatures. The finding that there are conditions where electric fields significantly affect enzyme inactivation highlights the importance of thoroughly assessing effects of alternative processing technologies on targets and indicators in food processing.