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Recent studies of zirconium isotopes in igneous systems have revealed significant mass dependent variability, the origin of which remains intensely debated. While magmatic zircon crystallisation could potentially drive equilibrium isotope fractionation, given that Zr4+ undergoes a shift in coordination as zircon precipitates from a silicic melt, ab initio calculations predict only limited equilibrium fractionation between zircon and melt at magmatic temperatures. To resolve this debate, we determined the isotopic fractionation between co-existing zircon and silicic melt using controlled zircon growth experiments. Our experimental results indicate that zircon has a lower δ94/90Zr relative to co-existing melt by ∼0.045 ‰ at magmatic conditions, which is in excellent agreement with ab initio predictions. Our results imply that, for most natural systems studied to date, the observed variability is predominantly a result of non-equilibrium rather than equilibrium isotope fractionation during zircon crystallisation.