The paradigm of cavity QED is a two-level emitter interacting with a high quality factor single mode optical resonator. The hybridization of the emitter and photon wave functions mandates large vacuum Rabi frequencies and long coherence times; features that so far have been successfully realized with trapped cold atoms and ions and localized solid state quantum emitters such as superconducting circuits, quantum dots, and color centers 1,2 . Thermal atoms on the other hand, provide us with a dense emitter ensemble and in comparison to the cold systems are more compatible with integration, hence enabling large-scale quantum systems. However, their thermal motion and large transit time broadening is a major challenge that has to be circumvented. A promising remedy could benefit from the highly controllable and tunable electromagnetic fields of a nano-photonic cavity with strong local electric-field enhancements. Utilizing this feature, here we calculate the interaction between fast moving, thermal atoms and a nano-beam photonic crystal cavity (PCC) with large quality factor and small mode volume. Through fully quantum mechanical calculations, including Casimir-Polder potential (i.e. the effect of the surface on radiation properties of an atom) we show, when designed properly, the achievable coupling between the flying atom and the cavity photon would be strong enough to lead to Rabi flopping in spite of short interaction times. In addition, the time-resolved detection of different trajectories can be used to identify single and multiple atom counts. This probabilistic approach will find applications in cavity QED studies in dense atomic media and paves the way towards realizing coherent quantum control schemes in large-scale macroscopic systems aimed at out of the lab quantum devices.