We consider Stokes systems in non-divergence form with measurable coefficients and Lions-type boundary conditions. We show that for the Lions conditions, in contrast to the Dirichlet boundary conditions, local boundary mixed-norm $L_{s,q}$-estimates of the spatial second-order derivatives of solutions hold, assuming the smallness of the mean oscillations of the coefficients with respect to the spatial variables in small cylinders. In the un-mixed norm case with $s=q=2$, the result is still new and provides local boundary Caccioppoli-type estimates, which are important in applications. The main challenges in the work arise from the lack of regularity of the pressure and time derivatives of the solutions and from interaction of the boundary with the nonlocal structure of the system. To overcome these difficulties, our approach relies heavily on several newly developed regularity estimates for parabolic equations with coefficients that are only measurable in the time variable and in one of the spatial variables.