The primary objective of navigation systems is to optimise component alignment to improve total knee replacement (TKR) performance. This study utilizes finite element analysis techniques to determine how component alignment affects tibial insert contact stresses. Contact stresses were derived from navigation system and conventional TKR alignments, and were compared to ideally aligned components. This study builds upon the work of a previous study, in which post-operative CT scans from 70 patients were utilized to extract knee component angular alignments. These patients had been randomised to having either navigation based or conventional TKR. Knee component finite element models were oriented into specific alignment positions. Tibial insert contact stresses were computed under physiologically relevant loads at various flexion angles. Finite element analysis was also performed on ideally aligned cases for comparison purposes. At full extension, the median alignment of conventional TKR induces contact stresses 17.8% above ideal alignment conditions. Navigation based TKR alignment induces stresses 3.5% above ideal alignment conditions. At 45–90° flexion, conventional TKR alignment induces stresses 2.7% above ideal alignment conditions, while comparable navigation based TKR alignment induces stresses that match ideal alignment conditions. Knee component alignment is improved by navigation techniques. This predictive finite element analysis study shows markedly reduced contact stresses for navigation aligned TKR compared to conventional aligned technique. The reduction in tibial insert contact pressures could reduce abnormal polyethylene wear, increasing the structural longevity of knee system components.