We consider $N$ by $N$ deformed Wigner random matrices of the form $X_N=H_N+A_N$, where $H_N$ is a real symmetric or complex Hermitian Wigner matrix and $A_N$ is a deterministic real bounded diagonal matrix. We prove a universal Central Limit Theorem for the linear eigenvalue statistics of $X_N$ for all mesoscopic scales both in the spectral bulk and at regular edges where the global eigenvalue density vanishes as a square root. The method relies on the characteristic function method in [47], local laws for the Green function of $X_N$ in [3, 46, 51] and analytic subordination properties of the free additive convolution [24, 41]. We also prove the analogous results for high-dimensional sample covariance matrices.