The AGILE (Advanced enerGetic Ion eLectron tElescope) project focuses on the development of a compact low-cost space-based instrument to measure the intensities of charged particles and ions in space. Using multiple layers of fast silicon sensors and custom front-end electronics, the instrument is designed for real-time particle identification of a large variety of elements from H to Fe and spanning energies from 1 to 100 MeV per nucleon. The robust method proposed in this work uses key defining features of electronic signals generated by charged particles (ions) traveling through silicon layers to reliably identify and characterize particles in situ. AGILE will use this real-time pulse shape discrimination technique for the first time in space based instrumentation. •Pulse shape discrimination is used to identify ions and measure their energy.•First application of pulse shape discrimination for space-based instrumentation.•Single silicon detector can be used for pulse shape discrimination.•Detailed end-to-end simulation of fast silicon detectors and electronics performed.