Aim To quantitatively assess corneal endothelial changes after phacoemulsification with the fluid-based system compared to conventional ultrasound technique. Methods This prospective, randomized clinical study included patients with cataract who were randomly assigned either to have phacoemulsification with the fluid-based system (30 eyes of 30 patientsFGroup 1) or with traditional ultrasound (30 eyes of 30 patientsFGroup 2). Patients who were available at each follow-up visit (25 eyes in both groups) were enrolled in the statistical analysis. Endothelial function was evaluated by measuring central corneal thickness, central endothelial cell density (ECD), mean cell size, and coefficient of variation in cell size preoperatively, 10 days, 1 and 3 months, and 1 year after surgery. Statistical analyses were performed using two-way repeated measure ANOVA. Results An acute, reversible increase of central corneal thickness (CCT) was found 10 days after surgery, which was similar in both groups (P ¼ 0.35). ECD decreased, whereas mean cell size increased significantly immediately after surgery. However, the impairments were finished after 1 month. The alterations were similar in both groups (ECD: P ¼ 0.99; mean cell size: P ¼ 0.85). The coefficient of variation in cell size remained stable after surgery (P ¼ 0.08), and significant difference was not found between groups (P ¼ 0.99). The endothelial cell loss (ECL) was 6.578.4% in Group 1 and 6.5711.7% in Group 2 (P ¼ 0.69). Conclusions Corneal endothelial changes were similar using the fluid-based system compared to the traditional ultrasound technique. The fluid-based method proved to be as safe as conventional ultrasound in cataract surgery.