Background: The navicular bone is a complex structure with a three-dimensional morphology that varies according to foot phenotype, but has not been completely characterized for safe percutaneous fixation. Objective: The objective of this study was to develop and apply a standardized 3D-CT protocol to identify the navicular safe bony corridor and quantify its dimensions according to foot phenotype and sex differences. Methods: Using an exploratory cross-sectional observational study, we evaluated 63 navicular bones (21 per phenotype: neutral, cavus, planus), selected by stratified random sampling. A pilot phase was first conducted on nine feet (three per phenotype) to establish and refine the measurement protocol; in this phase, measurements were independently performed by two observers, yielding an excellent inter-observer reliability. The remaining 54 feet were then measured by the biomedical engineer. Comparisons between foot phenotypes and sex were performed using Kruskal–Wallis and Dunn’s post hoc tests with a Bonferroni correction (all two-tailed, α = 0.05). Results: The safe bony corridor demonstrated median dimensions of a 38.96 mm length (range: 34.05–47.3 mm), a 10.02 mm diameter (range: 5.84–13.04 mm), and a volume of 3063 mm³ (range: 1135–5614 mm³). There were no differences in the volume among the phenotypes (p = 0.274), although their length differed (p = 0.046). The central corridor angle showed significant variation among the phenotypes (p = 0.010): cavus, 8.02°; neutral, 7.05°; planus, 6.99°. Corridor occupation varied by phenotype: cavus, 30.9%; neutral, 29.0%; planus, 27.2% (p = 0.008). Males demonstrated longer corridors than females (40.14 vs. 37.76 mm, p < 0.001), but a similar diameter (p = 0.085). The safe diameter (2 mm margin) median was 8.02 mm. Conclusions: A standardized and reproducible 3D-CT protocol allows for the precise identification of the safe navicular bony corridor for percutaneous screw fixation with a medial-to-lateral orientation. Although the corridor dimensions remained relatively consistent among phenotypes, the angular and dimensional variability by foot phenotype and sex justifies an individualized preoperative evaluation using 3D-CT to optimize implant selection.