The clockwork mechanism, which can naturally explain the origin of small numbers, is implemented in $SO(10)$ grand unified theories to address the origin of hierarchies in fermion masses and mixings. We show that a minimal Yukawa sector involving a $10_H$ and $overline{126}_H$ of Higgs bosons, extended with two clockwork chains consisting of $16+overline{16}$ vector-like fermions, can explain the hierarchical patterns with all the Yukawa couplings being of order one. Emergence of a realistic mass spectrum does not require any symmetry that distinguishes the three generations. We develop clockwork-extended $SO(10)$ GUTs both in the context of SUSY and non-SUSY frameworks. Implementation of the mechanism in non-SUSY scenario assumes a Peccei-Quinn symmetry realized at an intermediate scale, with the clockwork sector carrying non-trivial charges, which solves the strong CP problem and provides axion as a dark matter candidate.
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