AIM: To compare long-term postoperative outcomes of manual and femtosecond assisted corneal trephination in deep anterior lamellar keratoplasty (FS-DALK) for keratoconus. METHODS: In the retrospective study, 17 consecutive eyes that underwent vertical side cut incision FS-DALK and 22 eyes that underwent trephine incision DALK were collected over a 2-year period. Main measurements included postoperative uncorrected-visual acuity (UCVA), corrected distance visual acuity (CDVA), refractive sphere and cylinder, manifest refraction spherical equivalent (MRSE), flat and steep corneal keratometry (K1 and K2), endothelial cell density (ECD), and time of epithelium healing and suture removal. RESULTS: Groups were comparable for diagnosis and preoperative visual acuity. Follow-up averaged 23mo (range, 12-36mo). At 12mo, the mean UCVA was better in the manual-DALK group (P=0.039), and the refractive sphere was lower in the FS-DALK group (P=0.040). MRSE between groups differed at 1, 6, and 12mo postoperatively (P=0.047, 0.025, 0.042, respectively). Mean CDVA, cylinder, K1, K2, corneal astigmatism, ECD, and time of epithelium healing were similar between groups. Stability of MRSE, ECD, and K1 returned sooner after FS-DALK. Initial loosened suture removal time was earlier in the manual-DALK group (P=0.042) while complete suture removal time was similar (P=0.122). CONCLUSION: Manual and femtosecond assisted corneal trephination in DALK are options for advanced keratoconus. FS-DALK do not result in improved visual acuity but it is more stable during the follow-up period. FS-DALK in the present form show limited benefit, so surgical design and parameters still need to be optimized and explored.