In both quantum optics and cold atom physics, the behaviour of bosonic photons and atoms is often treated using phase space methods, where mode annihilation and creation operators are represented by c-number phase space variables, with the density operator equivalent to a distribution function of these variables. The anti-commutation rules for fermion annihilation, creation operators suggest the possibility of using anti-commuting Grassmann variables to represent these operators. However, in spite of the seminal work by Cahill and Glauber and a few applications, the use of Grassmann phase space methods in quantum–atom optics to treat fermionic systems is rather rare, though fermion coherent states using Grassmann variables are widely used in particle physics.The theory of Grassmann phase space methods for fermions based on separate modes is developed, showing how the distribution function is defined and used to determine quantum correlation functions, Fock state populations and coherences via Grassmann phase space integrals, how the Fokker–Planck equations are obtained and then converted into equivalent Ito equations for stochastic Grassmann variables. The fermion distribution function is an even Grassmann function, and is unique. The number of c-number Wiener increments involved is 2n2, if there are n modes. The situation is somewhat different to the bosonic c-number case where only 2n Wiener increments are involved, the sign of the drift term in the Ito equation is reversed and the diffusion matrix in the Fokker–Planck equation is anti-symmetric rather than symmetric. The un-normalised B distribution is of particular importance for determining Fock state populations and coherences, and as pointed out by Plimak, Collett and Olsen, the drift vector in its Fokker–Planck equation only depends linearly on the Grassmann variables. Using this key feature we show how the Ito stochastic equations can be solved numerically for finite times in terms of c-number stochastic quantities. Averages of products of Grassmann stochastic variables at the initial time are also involved, but these are determined from the initial conditions for the quantum state. The detailed approach to the numerics is outlined, showing that (apart from standard issues in such numerics) numerical calculations for Grassmann phase space theories of fermion systems could be carried out without needing to represent Grassmann phase space variables on the computer, and only involving processes using c-numbers. We compare our approach to that of Plimak, Collett and Olsen and show that the two approaches differ.As a simple test case we apply the B distribution theory and solve the Ito stochastic equations to demonstrate coupling between degenerate Cooper pairs in a four mode fermionic system involving spin conserving interactions between the spin 1/2 fermions, where modes with momenta −k,+k—each associated with spin up, spin down states, are involved.