In myopia, biometry including the axial length is important, along with the refractive data. We compared the rates of myopic regression 3 years after phakic intraocular lens (pIOL) implantation and laser in situ keratomileusis (LASIK) after matching the preoperative axial length in highly myopic eyes of Japanese patients. This retrospective nonrandomized study included 133 eyes of 84 patients with myopia exceeding -6.00 diopters (D) who underwent implantation of two iris-fixated pIOLs (pIOL group, 66 eyes/46 patients) or myopic LASIK (LASIK group, 67 eyes/38 patients) who were followed for more than 3 years postoperatively. The patient age, preoperative refraction, and preoperative axial length were matched between the study groups. There were no significant differences preoperatively between the groups in age, intraocular pressure, refraction, keratometry, or axial length. The mean regression values after 3 years compared with the 1-month postoperative refractions were -0.12 ± 0.47 (SD) D in the pIOL group and -0.82 ± 0.69 D in the LASIK group (p < 0.001). The differences in the mean regression rates between 1 and 12 months, 12 and 24 months, and 24 and 36 months of follow-up were, respectively, 0.09 ± 0.38 D, -0.11 ± 0.35 D, and -0.11 ± 0.30 D in the pIOL group and -0.57 ± 0.84 D, -0.24 ± 0.47 D, and 0.00 ± 0.53 D in the LASIK group (p < 0.001, p = 0.07, p = 0.15, respectively). There was a significant difference in myopic regression 3 years postoperatively between the groups matched for preoperative axial length in Japanese patients. This result has the potential to elucidate myopia in the future.