Modern proton therapy affords control of the delivery of radiotherapeutic dose on fine length and temporal scales. The authors have developed a novel detector technology based on Micromesh Gaseous Structure (Micromegas) that is uniquely tailored for applications using therapeutic proton beams. An implementation of a prototype Micromegas detector for Monte Carlo using Geant4 is presented here. Comparison of simulation results with measurements demonstrates agreement in relative dose along the proton longitudinal dose profile to be 1%. The effect of a radioactive calibration source embedded in the chamber gas is demonstrated by measurements and reproduced by simulations, also at the 1% level. Our Monte Carlo simulations are shown to reproduce the time structure of ionization pulses produced by a double-scattering delivery system.