This study was undertaken to compare the clinical and radiological outcomes achieved using total knee arthroplasty (TKA) with and without a navigation system. This study included 43 TKAs performed with a navigation system and 42 TKAs without a navigation system with a minimum two-year follow-up. We compared clinical outcomes including range of motion, Hospital for Special Surgery (HSS) and Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at the final follow-up. For radiological comparisons, we evaluated radiological alignment on standing radiographs of knees. HSS and WOMAC scores showed significant improvements at final follow-ups in both groups, but showed no significant inter-group differences (p > 0.05). Similarly, no significant differences were observed in range of motion (p = 0.962). TKAs performed with navigation showed significantly better outcomes in terms of mechanical angle and prosthetic alignment outliers than TKAs performed without navigation. However, we could not find any differences in functional outcomes between TKAs performed with or without a navigation system.