We study the dynamics of many-body Fermi systems, for a class of initial data which are close to quasi-free states exhibiting a nonvanishing pairing matrix. We focus on the mean-field scaling, which for fermionic systems is naturally coupled with a semiclassical scaling. Under the assumption that the initial datum enjoys a suitable semiclassical structure, we give a rigorous derivation of the time-dependent Hartree-Fock-Bogoliubov equation, a nonlinear effective evolution equation for the generalized one-particle density matrix of the system, as the number of particles goes to infinity. Our result holds for all macroscopic times, and provides bounds for the rate of convergence.