A CFD program is converted and modified to explore unsteady flow within the intake system of a pulse detonation engine (PDE). Using a quasi-one-dimensional approach the program provides insight into the unsteady nature of localized equivalence ratios to include their effects on PDE performance. The original FORTRAN program is converted into the MATLAB architecture, taking full advantage of user availability and post processing convenience. The converted program was validated against the original program and modified to include a primitive intake manifold system with a single fuel injector located approximately 10 feet upstream of the primary intake valve. Constant fuel mass flow rate at the injector end creates local variations in equivalence ratio throughout the PDE that may have significant impact on overall engine performance. The results of the current thesis research suggest that performance effects of up to 21% can be attributed to non-uniform fuel distribution throughout the detonation process and are most prevalent at lower frequencies and fill ratios.