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Abstract Background To evaluate the efficiency and practicality of femtosecond laser assisted cataract surgery (FLACS) in a public teaching hospital setting using a mobile FLACS system compared to conventional phacoemulsification cataract surgery (CPCS). Methods Ninety eyes from 90 patients underwent either FLACS or CPCS (45 in each group). Cataracts were graded using the Lens Opacities Classification System III system. Outcome measures included total surgery duration, femtosecond laser treatment time, vacuum time (VT), total phacoemulsification time (TPT) and total phacoemulsification power (TPP). Results No differences were observed in the preoperative mean cataract grades and co-morbidities. FLACS took longer than CPCS with a mean difference of 5.2 ± 4.5 min (range: 0–18.8 min). The average femtosecond laser treatment time was 4.3 ± 3.4 min (range: 1–15.5 min). The VT was 2.51 ± 0.45 min (range: 1.59–4.10 min). Although not significant, TPT in FLACS showed a trend towards improvement (mean 1.0 ± 0.6 s; range: 0.1–2.4 s) compared to CPCS (mean 1.2 ± 0.6 min; range: 0.5–2.5 min). Whereas, TPP was significantly less in FLACS (mean 17.9 ± 5.0%; range: 5–27%) compared to CPCS (mean 20.3 ± 4.1%; range: 12.0–28.7%)(p = 0.031). Conclusions The mobile FLACS system housed in the same operating room increased the surgical duration by 5.2 min. The average VT was 2.51 min, which was lower in comparison to published experience using non-mobile FLACS systems.