Background: Knee osteoarthritis (KOA) progression is often influenced by biomechanical factors. Biomechanical interventions, such as Trunk stabilization exercise (TSE) and Mulligan joint mobilization (MWM), may offer relief from KOA symptoms and potentially slow disease progression. However, the comparative efficacy of these therapies remains uncertain. This study aimed to compare the efficacy of TSE, Mulligan joint mobilization, and isometric knee strengthening (KSE) on disability, pain severity, and aerobic exercise capacity in patients with KOA. Methodology: A randomized controlled trial (RCT) with three intervention groups was conducted between September 2020 to February 2021. The study enrolled adults aged between 40 and 60 years with a confirmed KOA diagnosis recruited from the physical therapy clinic of the Sindh Institute of Physical Medicine and Rehabilitation, Pakistan. Participants were randomly assigned to receive 24 sessions of either TSE, MWM, or KSE. The knee's functionality was assessed using the Knee Injury and Osteoarthritis Outcome Score (KOOS), pain on a visual analogue scale (VAS), and two objective functional tests—the 6-minute walk test (6MWT) and the 11-stair climb test (SCT). These assessments were conducted at baseline, the third week, and the sixth week. Changes in outcome measures were analyzed using a mixed-design ANOVA with Bonferroni post-hoc analysis, with statistical significance set at a p-value < 0.05. Result: Of the 60 participants, 22 (36.7%) were females, and 38 (63.3%) were males. Within-group analysis revealed a significant improvement in all outcome measures at the third week (p < 0.05) and sixth week (p < 0.05). Notably, the TSE group exhibited a greater reduction in mean difference (M.D) in VAS scores than the MWM and KSE groups across various measures in the third week. At rest, during stair ascent, and descent, the TSE group showed significant improvements in VAS scores: MWM (-2.05; -1.94; -1.94), TSE (-2.38; -2.5; -2.5), KSE (-1.05; -0.63; -0.63). Additionally, during sub-maximal exercise capacity assessment, the TSE group showed greater improvement (MWM 12.89; TSE 22.68; KSE 7.89), as well as in Knee Injury and Osteoarthritis Outcome Score for activities of daily living (KOOS-ADL) (MWM 20.84; TSE 28.84; KSE 12.68), and KOOS-pain (MWM 24.84; TSE 27.77; KSE 5.77) at the third-week assessment (p < 0.05). The TSE group demonstrated significant improvements (p < 0.05) across various measures in the sixth week. Specifically, improvements were observed in VAS scores at rest (MWM − 4.15; TSE − 4.42; KSE − 3.78), during stair ascent (MWM − 3.89; TSE − 4.88; KSE − 3.56) and descent (MWM − 3.78; TSE − 4.05; KSE − 2.94). Furthermore, significant improvements were noted in the stair climb test (MWM − 7.05; TSE − 7.16; KSE − 4.21), 6-minute walk test (6MWT) (MWM 22.42; TSE 37.6; KSE 13.84), KOOS-pain (MWM 41.47; TSE 49.11; KSE 28.73), and KOOS-ADL (MWM 40.31; TSE 50.57; KSE 26.05). Conclusion: In this study in patients with KOA, TSE had greater efficacy compared to MWM and KSE in enhancing functional levels, reducing pain, improving sub-maximal exercise capacity, and performance on the stair climb test. Importantly, mean scores between the groups, particularly in the TSE group, reached the minimally important level, particularly in key areas such as pain, functional levels, sub-maximal exercise capacity, and stair climb performance. Clinicians should consider the significant pain reduction, improved functionality, and enhanced exercise capacity demonstrated by TSE, indicating its potential as a valuable therapeutic choice for individuals with KOA. Trial no: ClinicalTrials.gov = NCT04099017 23/9/2019. [ABSTRACT FROM AUTHOR]