Traumatic brain injury (TBI) is a leading cause of mortality and disability worldwide. Accurate estimation of the post-injury survival interval is essential for reconstructing events, while in clinical neurotraumatology the first 24 h are recognized as a critical window for deterioration. Mast cells (MCs), identifiable by CD117 (c-Kit), and the transcription factor hypoxia-inducible factor 1-alpha (HIF-1α) are key players in neuroinflammation and hypoxic cascades, yet their temporal expression in human TBI remains poorly defined. We investigated 40 forensic autopsy cases with survival intervals ranging from minutes to 16 days. Immunohistochemistry for CD117 and HIF-1α was performed on peri-contusional cortex and white matter. CD117-positive cells exhibited a biphasic perivascular pattern: an early peak within 1–4 h, decline by 19 h, and reappearance at 4–8 days. Intraparenchymal CD117-positive cells, often with glial or neuronal morphology, were abundant in survival < 19 h, declined by day 4, and reappeared at day 16. In contrast, HIF-1α was absent before 19 h (except focal CA1 positivity in a hypoxic–anoxic case), then emerged in endothelial cells at 19 h, extended to neurons by 2 days, peaked in vessels at day 6, shifted to macrophages at 7–8 days, and localized to glial cells at 16 days. These findings demonstrate that CD117 and HIF-1α follow complementary, time-dependent trajectories after TBI, acting as molecular clocks for survival interval estimation. Their dynamics mirror the clinical critical window at 18–24 h, underscoring their translational value in both forensic and clinical settings.