Numerical investigation of a sonic reaction control jet interacting with the high-speed cross-flow has been carried out over a generic missile body. Simulations are performed in the early-hypersonic slip flow regime for air, CO2, and helium jet gases. An open source computational fluid dynamics tool, OpenFOAM is used to model the steady state, three-dimensional compressible Navier–Stokes equations with k-ω shear stress transport turbulence model. The conventional computational fluid dynamics solver is extended with additional features, such as transport of species, nonequilibrium boundary conditions for velocity slip and temperature jump, and a heat load calculation utility based on the sliding friction effect. The extended solver is validated with the direct simulation Monte Carlo results for the case of a sonic argon jet injected into hypersonic nitrogen cross-flow. The extended solver is able to accurately capture all the qualitative flow features like separation shock, bow shock, and barrel shock, and it also improves heat load predictions in the slip flow regime. The main objective of the present work is to study the effect of rarefaction and change in jet gas species on the complex flow topology, heat load distribution, and spread of jet gas on the missile body. Heat load predictions are found to be strongly dependent on the slip velocity of molecules in addition to the temperature gradient near the wall. The strength of a bow shock and a barrel shock is higher for helium jet, compared to air and CO2 jets, which spread more along the missile body, and weaker shocks and reduced heat load is generated. The current work is significant from the perspective of the thermal design of spacecraft surfaces and positioning of the optical sensors. © IMechE 2019.