This theoretical study recorded the influence of the distributed injection of hydrogen through a permeable surface and its combustion on the stability and transition of a supersonic boundary layer (BL). The laminar base flow for a multicomponent flat-plate BL was computed using the computational fluid dynamics solver with finite-rate chemistry for free-stream Mach number (M) = 2. Linear stability theory (LST) equations for a reactive gas mixture were derived in the local parallel base flow approximation. Stability calculations based on the developed theory revealed the possibility of a decrease in the local spatial amplification rates of unstable perturbations. A double reversal in the maximal amplification rate magnitudes of perturbations was obtained, wherein at first, they increased, then decreased to zero, and then rose again. The influence of the distributed injection and combustion of hydrogen in the supersonic BL on the position of the laminar-turbulent transition was estimated using the LST-based eN-method. Calculated and experimentally obtained dependencies of the relative transition Reynolds number on the relative mass flow rate of injected hydrogen were compared. It was found that depending upon the flow conditions, the hydrogen diffusion flame could accelerate or decelerate the transition in the supersonic M = 2 BL, when compared to absence of hydrogen burning. Two counteracting effects compete: heat supply by combustion exerts stabilizing influence, while low-molecular-weight gas blowing from the surface exerts destabilizing influence. Depending on the interplay of these two factors, it would be possible to obtain acceleration or deceleration of transition.