The recent findings of increased Choroidal Thickness (CT) in Keratoconus (KC) patients raised the question of whether CT could be an indicator of progressive KC. To test this hypothesis, we evaluated and compared the choroidal profile in progressive and non-progressive KC. We ran a cross-sectional observational study in 76 patients diagnosed with KC, age 14–30, to assess KC progression. Progression was defined as when at least two of the studied variables confirmed progression (Kmax, Km, PachyMin, D-Index, Astig, K2, 3 mm PCR). Included patients performed a Spectralis Optical Coherence Tomography (OCT) with enhanced depth image (EDI) technology to evaluate choroidal profile. Choroidal measurements were taken subfoveally and at 500 µm intervals from the fovea, in 7 different locations, and compared between groups. Multivariate linear regression analyses were also performed to assess the influence of CT in KC progression. Thirty-six eyes (47.4%) were classified as KC progressors. The mean subfoveal CT observed in the total sample was 382.0 (± 97.0) μm. The comparison between groups (progressive and non-progressive KC) showed no differences in the locations evaluated (mean subfoveal CT difference between groups was 2.4 μm, p = 0.915). In the multivariate analysis CT seems not be influenced by KC progression (B = 6.72 μm, 95% CI − 40.09 to 53.53, p = 0.775). Assessment of choroidal profile does not appear to be a useful tool to differentiate progressive and non-progressive KC. Further research is needed in order to better understand the role of choroid in KC.