Quarkonium production mechanism in high multiplicity small collision systems has recently been pursued in the color-glass-condensate (CGC) effective theory combined with non-relativistic QCD (NRQCD) factorization, allowing to study initial state interactions. Quarkonium polarization, potentially measured in future experiments, would help elucidate the quarkonium production mechanism at high multiplicities. In this paper, we provide predictions on $J/psi$ polarization parameters in high multiplicity proton-proton ($pp$) and proton-nucleus ($pA$) collisions within the CGC+NRQCD framework. Theoretical predictions are given for $J/psi$ rapidity $2.5< y_{J/psi}<4$, charged-particle multiplicity pseudorapidity $|eta_{ch} | <1$ and energies $sqrt{S}=13mathrm{~TeV}$ for $pp$, $sqrt{S}=8.16mathrm{~TeV}$ for $pA$ collisions. Considering two leptonic frame choices (Collins - Soper and helicity) we find a weak polarization of $J/psi$ that additionally decreases with growing event activities. No significant system size dependence between $pp$ and $pA$ collisions is obtained - this could be a new constraint to initial state interactions in small collision systems.
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