Purpose A key part of kinematic alignment (KA) and functional alignment (FA) is to restore the natural femoral joint line, in particular the medial joint line. KA is known to reproduce the femoral joint line accurately; however, direct comparisons with other surgical techniques such as FA are currently lacking. The purpose of this study was to evaluate diferences of alignment parameters in KA and FA techniques with a special focus given to the femoral joint line. Methods We performed a retrospective radiological analysis of pre-and postoperative long leg radiographs of 221 consecutive patients with varus or neutral leg alignment, who underwent primary total knee arthroplasty (TKA) procedures from 2018 to 2020. Patients were assigned to one of four groups: (1) FA: image-based robotic-assisted TKA, (2) FA: imageless robotic-assisted TKA, (3): restricted KA: 3D cutting block-assisted (patient-speciic instruments, PSI) TKA, (4): unrestricted KA: calipered technique. Patients' radiographs were (re)-analyzed for overall limb alignment, medial proximal tibial angle (MPTA), lateral distal femoral angle (LDFA), as well as medial and lateral femoral joint line alteration. Statistical signiicance was determined using unpaired t testing (FA vs. KA group) and one-way ANOVA (subgroup analyses). Results Comparisons of KA vs. FA, as well as individual subgroups of KA and FA did not show any diferences in the accuracy of medial joint line reconstruction (< 2 mm, p = 0.384, p = 0.744, respectively) and LDFA alteration (< 2°, p = 0.997, 0.921, respectively). Correction of MPTA (3.4° vs. 2.2°) and lateral femoral joint line (2.1 mm vs. 1.5 mm) was higher for FA and FA subgroups compared to KA and KA subgroups (both p < 0.001). Conclusion Kinematic and functional alignments showed a comparable accuracy in reconstruction of the medial femoral joint line and femoral joint line orientation. Increased correction of MPTA and lateral femoral joint line was recorded with FA techniques. Level of evidence III.