The Extreme Universe Space Observatory on a Super Pressure Balloon II (EUSO-SPB2) measured extensive air showers (EASs) from upward-going High Energy Cosmic Rays by flying a Cherenkov Telescope (CT) at 33 km altitude. The telescope could be tilted just above the Earth’s limb, 5.8° below horizontal, and 650 km away as viewed from the balloon. This configuration enables the detection of EASs that develop over a longer path length than downward-going showers. The lifetime of 100 GeV muons, as an example, corresponds to a path length of 620 km in Earth’s upper atmosphere, where there is a decreased amount of energy lost due to atmospheric interactions (only ≈ 40 MeV/km lost at 15 km altitude). In this configuration, muons can travel hundreds of kilometers while bending in Earth’s geomagnetic field before they decay. These effects cause EASs to be more dense with muons at larger shower depths compared to the shower at Xmax, a result known as the muon tail. The objective of this simulation is to understand whether the CT on EUSO-SPB2 could measure the Cherenkov signal produced by the muon tail and observe the effects of the muons deflecting in Earth’s geomagnetic field. We found that the timing and angular distributions of the Cherenkov signal allow the muon component to be separated from the main Cherenkov signal and we identified quantifiable effects of the muons deflecting in the geomagnetic field. However, at this time we are unable to simulate enough events to analyze the distribution of photons arriving in an area the size of the aperture of the CT. Thus, we cannot make conclusions about whether these effects can be seen by EUSO-SPB2.