There is an increasing incidence, prevalence, and burden of knee osteoarthritis due to a global increase in obesity and an aging population. The aim of the present study was to compare the effectiveness of the addition of aerobic exercises performed in an unloaded or loaded position to a conventional exercise program in overweight subjects with knee osteoarthritis. Twenty-four subjects were randomly allocated to receive 36 sessions of 30-min duration of either sitting aerobic exercises (experimental group) or standing aerobic exercises (control group). Pain intensity, knee disability, and quality-of-life data were collected at baseline and at 12, 24, and 36 sessions. Generalized linear mixed models (GLMMs) were constructed for the analysis of the differences. Significant differences were found in the experimental group for self-reported pain and knee pain and disability at 24 and 36 sessions (p < 0.05). Significant between-group differences were observed in change in self-reported knee pain and disability and quality of life from baseline to 24th- and 36th-session measurements in favor of the experimental group. Adherence to treatment was higher in the experimental group. Adding aerobic exercises in an unloaded position to a conventional exercise program produced superior effects over time for self-reported knee pain, knee pain and disability and quality of life compared to loaded aerobic exercises in overweight subjects with knee osteoarthritis.