Abstract The divergent representation of ocean net primary productivity (NPP) in Earth system models (ESMs) causes uncertainty in NPP projections, which must be reduced to effectively inform marine management and climate mitigation strategies. Here, we investigate the sources of uncertainty in monthly‐mean NPP by seven ESMs under four emissions scenarios. We find that ESM disagreement on the preindustrial mean NPP in low‐mid latitudes and on the preindustrial seasonal cycle of NPP in high latitudes dominates the uncertainty in absolute NPP, which remains quasi‐constant under climate change. Uncertainty in the NPP anomaly (NPPA) relative to the preindustrial state doubles on average from 1850 to 2100, due to increased ESM disagreement on the shifted decadal mean in low‐mid latitudes and shifted seasonal cycle in high latitudes. Constraining these emerging sources of model uncertainty would result in detectable NPPA climate signals by 2100 over a larger area of the global ocean.