Intramolecular isotope distributions, including isotope clumping and position specific fractionation, can provide proxies for the formation temperature and formation and destruction pathways of molecules. In this study, we explore the position-specific hydrogen isotope distribution in propane. We analyzed propane samples from 10 different petroleum systems with high-resolution molecular mass spectrometry. Our results show that the hydrogen isotope fractionation between central and terminal positions of natural propanes ranges from −102‰ to +205‰, a much larger range than that expected for thermodynamic equilibrium at their source and reservoir temperatures (36–63‰). Based on these findings, we propose that the hydrogen isotope structure of catagenic propane is largely controlled by irreversible processes, expressing kinetic isotope effects (KIEs). Kinetic control on hydrogen isotope composition of the products of thermal cracking is supported by a hydrous pyrolysis experiment using the Woodford Shale as substrate, in which we observed isotopic disequilibrium in the early stage of pyrolysis. We make a more general prediction of KIE signatures associated with kerogen cracking by simulating this chemistry in a kinetic Monte Carlo model for different types of kerogens. In contrast, unconventional shale fluids or hot conventional reservoirs contain propane with an isotopic structure close to equilibrium, presumably reflecting internal and/or heterogeneous exchange during high temperature storage (ca. 100–150 °C). In relatively cold (<100 °C) conventional gas accumulations, propane can discharge from its source to a colder reservoir, rapidly enough to preserve disequilibrium signatures even if the source rock thermal maturity is high. These findings imply that long times at elevated temperatures are required to equilibrate the hydrogen isotopic structure of propane in natural gas host rocks and reservoirs. We further defined the kinetics of propane equilibration through hydrogen isotope exchange experiments under hydrous conditions; these experiments show that hydrogen in propane is exchangeable over laboratory timescales when exposed to clay minerals such as kaolinite. This implies rather rapid transfer of propane from sources to cold reservoirs in some of the conventional petroleum systems. Propane is also susceptible to microbial degradation in both oxic and anoxic environments. Biodegradation of propane in the Hadrian and Diana Hoover oil fields (Gulf of Mexico) results in strong increases in central-terminal hydrogen isotope fractionation. This reflects preferential attack on the central position, consistent with previous studies.