We study a mathematical model describing 3D viscoelastic fluids with memory, fractional viscosity, and regularized by means of a horizontal anisotropic filter. This regularization is obtained through the action of the inverse of the horizontal Helmholtz operator, and the system is considered in a fully periodic space‐domain Ω. After introducing a controlled version of such a model, we take into account for it a suitable Galerkin approximation scheme. Exploiting the Hilbert uniqueness method, we establish the exact controllability of the finite‐dimensional Galerkin system.