Abstract Parameterizing boundary layer turbulence in Earth System Models (ESMs) introduces a key source of uncertainty. Here, we explore the impact of implementing a prognostic formulation (PMF) for momentum flux, which permits countergradient (CG) fluxes. We implement PMF in the turbulence parameterization in the Community Atmosphere Model version 6 (CAM6). CG fluxes in PMF reduce globally‐integrated momentum flux in CAM6. A similar response in globally‐integrated momentum flux is observed when reducing a tunable diffusivity parameter in the existing diagnostic formulation for momentum flux (DMF). Both methods of reducing effective eddy diffusivity produce qualitatively similar responses in the modeled general circulation, namely an enhanced upward branch of the Hadley cell, increased equatorward low‐level flow, and strengthened meridional temperature and moisture gradients. However, the reduction in effective eddy diffusivity from CG fluxes in PMF produces a higher‐magnitude response in the general circulation compared to reducing the diffusivity parameter in DMF.