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Transition frequencies of atoms and ions are among the most accuratelyaccessible quantities in nature, playing important roles in pushing thefrontiers of science by testing fundamental laws of physics, in addition to awide range of applications such as satellite navigation systems. Atomic clocksbased on optical transitions approach uncertainties of $10^{-18}$, where fullfrequency descriptions are far beyond the reach of the SI second. Frequencyratios of such super clocks, on the other hand, are not subject to thislimitation. They can therefore verify consistency and overall accuracy for anensemble of super clocks, an essential step towards a redefinition of thesecond. However, with the measurement stabilities so far reported for suchfrequency ratios, a confirmation to $1 \times 10^{-18}$ uncertainty wouldrequire an averaging time $\tau$ of multiple months. Here we report ameasurement of the frequency ratio of neutral ytterbium and strontium clockswith a much improved stability of $4 \times 10^{-16} ({\tau}/s)^{-1/2}$.Enabled by the high stability of optical lattice clocks interrogating hundredsof atoms, this marks a 90-fold reduction in the required averaging time over aprevious record-setting experiment that determined the ratio of Al+ and Hg+single-ion clocks to an uncertainty of $5.2 \times 10^{-17}$. For the Yb/Srratio, we find R = 1.207 507 039 343 337 749(55), with a fractional uncertaintyof $4.6 \times 10^{-17}$.

Frequency ratio of Yb and Sr clocks with $5 \times 10^{-17}$ uncertainty at 150 s averaging time