Resistance exercise effectively improves bone mineral density (BMD) and muscle quality (e.g., muscle mass and muscle strength). The present study aimed to examine the effect of a 24-week resistance exercise training (RT) program on body composition, BMD, functional fitness, and isokinetic muscle strength in obese older women. Forty obese older women were initially enrolled. Among them, 30 participants (age: 80.55 ± 4.94 years; body fat percentage: 36.25 ± 3.44%) completed the study. The participants were randomly assigned into two groups: the RT group (n = 15) and the control (CON) group (n = 15). The RT group participated in the exercise for 60 min per session and two sessions per week for 24 weeks. Pre-test and post-test body composition, BMD, functional fitness, and isokinetic muscle strength were evaluated. The RT group increased significantly in functional fitness (hand grip strength: 1.70 kg, < 0.01, and lower body strength: 3.87 n, < 0.001), and isokinetic muscle strength (non-dominant leg extensor peak torque %BW at 60°/s: 13.20%, < 0.05, dominant leg (DL) flexor peak torque at 60°/s: 3.87 Nm, < 0.05, and DL flexor peak torque %BW at 60°/s: 7.60%, < 0.05). However, the CON group showed negative changes in body composition (fat mass: 1.15 kg, < 0.001, body fat percentage: 1.59%, < 0.001, and fat-free mass: -0.58 kg, < 0.05), BMD (whole-body: -0.01 g/cm, < 0.001 and forearm: -0.01 g/cm, < 0.05), functional fitness (lower body flexibility: -3.23 cm, < 0.01, upper body strength: -2.06 n, < 0.01, and agility and dynamic balance: 0.54 s, < 0.01), and isokinetic muscle strength at 60°/s and 180°/s (all peak torque % body weight variables: -7.31--1.50, < 0.05). Our findings show that the CON group negatively affects body composition, BMD, functional fitness, and isokinetic muscle strength in obese older women for 24 weeks.