Abstract The inclusion of carbon cycle processes within CMIP5 Earth system models provides the opportunity to explore the relative importance of differences in scenario and climate model representation to future land and ocean carbon fluxes. A two-way analysis of variance (ANOVA) approach was used to quantify the variability owing to differences between scenarios and between climate models at different lead times. For global ocean carbon fluxes, the variance attributed to differences between representative concentration pathway scenarios exceeds the variance attributed to differences between climate models by around 2025, completely dominating by 2100. This contrasts with global land carbon fluxes, where the variance attributed to differences between climate models continues to dominate beyond 2100. This suggests that modeled processes that determine ocean fluxes are currently better constrained than those of land fluxes; thus, one can be more confident in linking different future socioeconomic pathways to consequences of ocean carbon uptake than for land carbon uptake. The contribution of internal variance is negligible for ocean fluxes and small for land fluxes, indicating that there is little dependence on the initial conditions. The apparent agreement in atmosphere–ocean carbon fluxes, globally, masks strong climate model differences at a regional level. The North Atlantic and Southern Ocean are key regions, where differences in modeled processes represent an important source of variability in projected regional fluxes.