This study investigated the optimization of exhaust system parameters for two-stroke engines in unmanned aerial vehicles, with a focus on improving performance at varying altitudes (sea level, 10,000 ft, and 21,000 ft). The research examined the impact of baffle plate hole diameter, header pipe length, and header pipe diameter on backpressure and exhaust flow dynamics. Two-stroke engines, while valued for their high power-to-weight ratio, suffer efficiency losses due to fresh air-fuel mixture leakage, particularly under reduced atmospheric pressure at high altitudes. The objective was to reduce backpressure-related inefficiencies by modifying three key exhaust parameters: baffle plate hole diameter, header pipe length, and header pipe diameter. Computational Fluid Dynamics simulations were performed in ANSYS Fluent using steady-state compressible flow assumptions, with boundary conditions replicating atmospheric pressures at sea level (1.013 bar), 10,000 ft (0.696 bar), and 21,000 ft (0.445 bar). Mesh independence validation was achieved with a final error margin of 0.01%, ensuring numerical accuracy. Important results show that decreasing the baffle plate hole diameter from 6 mm to 3 mm increases backpressure, enhancing scavenging efficiency but potentially raising exhaust temperature. At 21,000 ft, the optimal backpressure of 0.23 bar was achieved with a 4.6 mm baffle hole. Similarly, reducing header pipe length increased backpressure (0.105 bar at 122.5 mm vs. 0.09985 bar at 162.5 mm), while increasing header pipe diameter raised backpressure (0.104 bar at 36 mm vs. 0.097 bar at 24 mm). The optimal combination 4.6 mm hole, 122.5 mm length, and 36 mm diameter provides a favorable balance of flow resistance and scavenging, improving engine efficiency at high altitudes. These findings demonstrate that passive exhaust geometry tuning can effectively enhance UAV engine performance under altitude-induced pressure changes, offering a practical and scalable design approach. Unlike prior studies that focus on powertrain enhancements via turbocharging or fuel system control, this work offers a novel, passive exhaust geometry optimization strategy tailored to UAV engines. The study fills a critical research gap by systematically quantifying the relationship between exhaust configuration and altitude-dependent backpressure. Specific results include achieving a 0.23 bar backpressure at 21,000 ft using the optimized configuration, which allows for efficient engine operation without hardware modifications. This work contributes to lightweight, cost-effective unmanned aerial vehicle design by enabling high-efficiency performance without additional propulsion components, and the findings are presented in a manner accessible to a broad engineering audience.