Zinc (Zn) isotope data for mid-ocean ridge basalts (MORB) are scarce. The possible effects of MORB differentiation and mantle compositional heterogeneity on MORB Zn isotope compositions are poorly understood. In this paper, we report Zn isotope data of MORB lavas from the East Pacific Rise (EPR) at 10°30′N, which are understood to have been derived by a similar extent of melting from a compositionally uniform mantle source but manifest significantly varying extents of magma differentiation (MgO = 7.38–1.76 wt%) to demonstrate unequivocal Zn isotope fractionation during MORB differentiation. These lavas have a small δ66Zn (relative to the JMC-Lyon standard) range of 0.21–0.32‰, with an average of 0.26 ± 0.07‰ (2SD, N = 24), overlapping with literature data. However, δ66Zn values show significant correlations with indices of magma differentiation (e.g., MgO and CaO), with the more differentiated samples having isotopically heavier Zn. We can thus conclude that MORB differentiation can lead to ∼0.1‰ δ66Zn elevation, which is similar to that observed in Hawaiian Kilauea Iki lava lake samples. Fractional crystallization of olivine and clinopyroxene at MgO > ∼3.5 wt% and clinopyroxene and Fe–Ti oxides dominated by ilmenite at MgO < ∼3.5 wt% results in the observed Zn isotope fractionation. The δ66Zn values for primitive N-MORB and MORB source mantle are estimated to be ∼0.22‰ and ∼0.17‰, respectively. Furthermore, we observe a positive correlation between δ66Zn and [La/Sm]N in primitive (MgO = 7.58–9.01 wt%) literature MORB, indicating the existence of possible Zn isotope heterogeneity in the oceanic upper mantle. We thus predict heavy Zn isotope enrichment in mantle sources for E-MORB samples with high [La/Sm]N, which requires future testing.