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PURPOSE: To study the accuracy with which proton stopping power ratio (SPR) can be determined with dual-energy computed tomography (DECT) for small structures and bone-tissue-air interfaces like those found in the head or in the neck. METHODS: Hollow cylindrical polylactic acid (PLA) plugs (3 cm diameter, 5 cm height) were 3D-printed containing either one or three septa with thicknesses t(septa) = 0.8 mm, 1.6 mm, 3.2 mm and 6.4 mm running along the length of the plug. The cylinders were inserted individually into a tissue equivalent head phantom (16 cm diameter, 5 cm height). First, DECT scans were obtained using a Siemens SOMATOM Definition Edge CT scanner. Effective atomic number (Z(eff)) and electron density (ρ(e)) images were reconstructed from the DECT to produce SPR-CT images of each plug. Second, independent elemental composition analysis of the PLA plastic was used to determine the Z(eff) and ρ(e) for calculating the theoretical SPR (SPR-TH) using the Bethe-Bloch equation. Finally, for each plug, a direct measurement of SPR (SPR-DM) was obtained in a clinical proton beam. The values of SPR-CT, SPR-TH, and SPR-DM were compared. RESULTS: SPR-CT for PLA agreed with SPR-DM for t(septa) ≥ 3 mm (for CT slice thicknesses of 0.5 mm, 1.0 mm, and 3.0 mm). The density of PLA was found to decrease with thickness when t(septa) < 3 mm. As t(septa) (and density) decreased, the SPR-CT values also decreased, in good agreement with SPR-DM and SPR-TH. CONCLUSION: Overall, the DECT-based SPR-CT was within 3% of SPR-TH and SPR-DM in the high-density gradient regions of the 3D-printed plugs for septa greater than ~3mm in thickness.