In this paper, we present the results from a design study for an ultra-high resolution SPECT system with various aperture designs. The system uses a recently developed ultra-high resolution gamma camera based on an intensified Electron-multiplying Charge Coupled Device (EMCCD) sensor. It provides an intrinsic spatial resolution of <60um and a high signal-to-noise ratio for imaging the 27-35keV photons emitted by 1-125. The goal of present work is to optimize the multiple-pinhole aperture design for a stationary 4 headed SPECT system. The system is equipped with a variable aperture system that allows a large number of different aperture configurations to be used. In this study, we used the resolution-variance tradeoff as a performance index for selecting appropriate apertures for several imaging scenarios. A large number of apertures were compared with Monte Carlo simulations and experimental measurements.