Microbeam radiation therapy (MRT) is a new oncology method currently under development for the treatment of inoperable pediatric brain tumors. Monte Carlo simulation, or the computational study of radiation transport in matter, is often used in radiotherapy to theoretically estimate the dose required for treatment. However, its potential use in MRT dose planning systems is currently hindered by the significant discrepancies that have been observed between measured and theoretical dose and the PVDR (peak to valley dose ratio). The need to resolve these discrepancies is driven by the desirability of making MRT available to humans in the next few years. This article aims to resolve some of the discrepancies by examining the simplifications adopted in previous MRT Monte Carlo studies, such as the common practice of commencing microbeam transport on the surface of the target which neglects the influence of the distributed synchrotron source, multislit collimator, and the beam divergence between them. This article uses PENELOPE Monte Carlo simulation to investigate the influence of these beamline components upstream of the target on the lateral dose profiles and PVDRs of an array of 25 microbeams. It also compares the dose profiles and PVDRs of a microbeam array produced from a single simulation (full array) to those produced from the superposition of a single microbeam profile (sup array). The effect of modeling the distributed source and the beam divergence was an increase in the absorbed dose in the penumbral and valley regions of the microbeam profiles. Inclusion of the multislit collimator resulted in differences of up to 5 microm in the FWHM of microbeam profiles across the array, which led to minor variations in the corresponding PVDR yields.