To evaluate the impact of excimer laser-assisted deep anterior lamellar keratoplasty (Exc-DALK) and excimer laser-assisted penetrating keratoplasty (Exc-PKP) on subfoveal choroidal thickness (SFCT) in eyes with advanced keratoconus. A retrospective comparative clinical study, which compares the outcomes of 24 eyes treated with Exc-DALK (G1) against matched group of 43 eyes treated with Exc-PKP (G2) at both 2 months (T1) and 2 years (T2) postoperatively. Main outcomes included best-corrected visual acuity (BCVA), central macular thickness (CMT), and SFCT. Preoperatively, there were no significant differences between both groups regarding BCVA, CMT or SFCT (p > 0.05). There were no significant differences between both groups regarding BCVA at both follow-ups (p > 0.05). There were no significant differences between both groups regarding CMT at both follow-ups (p > 0.05). SFCT was higher in G2 than G1 at both follow-ups (p < 0.01). Compared to preoperative SFCT, there were no significant changes in SFCT in G1 at both follow-ups (p > 0.05). In G2, SFCT increased significantly at T1 (p < 0.01) and did not differ significantly at T2 (p = 0.17). SFCT increased significantly after Exc-PKP but not after Exc-DALK, which might indicate that Exc-DALK affects the choroid less and thus could represent a less traumatic approach to ocular tissue than Exc-PKP.