Background Cataract development is common in phakic eyes filled with silicone oil (SO), necessitating subsequent cataract removal. This study evaluated the refractive outcome in eyes filled with SO undergoing phacoemulsification cataract surgery (PCS). Methods This retrospective study evaluated patients with SO tamponade who were scheduled for PCS. Results Subjects (n=26) were followed-up for 29.5 ± 13.9 months after cataract surgery. The median spherical equivalent refraction (SER) was +5.3 D (interquartile range [IQR] +2.9 to +6.7) before PCS, and +3.4 D (IQR +2.0 to +4.4) after PCS. Within the follow-up period retinal reattachment after SO removal was achieved in 15 out of 26 eyes (57.7%). In 13 eyes assessment of refraction after SO-removal was possible, and showed a myopic shift of -4.6 D (IQR -2.9 to -7.3) in the SER. After SO removal, 5 of 13 eyes (38.5%) were within ±1.0 D of the target refraction, while 9 out of 13 eyes (69.2%) were within ±2.0 D. Conclusions The refractive outcome after PCS for eyes filled with SO is less predictable than that for normal eyes. Some of the eyes undergoing silicone oil injection may require long-term tamponade.