Background: Bird dog exercise (BDE) is one of the lumbar stabilization exercises that rehabilitate low back pain by co-contraction of the local and global muscles. Previous studies have reported the effect of various type of BDEs (for example, practicing the exercises on various surfaces and changing the limb movement) for muscle co-contraction. Objects: This study aimed to investigate the effect of knee joint flexion position of the raised lower limb on abdominal and back muscle activity during BDE in patients with chronic low back pain (CLBP). Methods: Thirteen males participated in this study (age: 32.54 ± 4.48 years, height: 177.38 ± 7.17 cm). Surface electromyographic (SEMG) data of the internal abdominal oblique (IO), external abdominal oblique (EO), lumbar multifidus (MF), and thoracic part of the iliocostalis lumborum (ICLT) were collected in two knee joint flexion positions (90° flexion versus 0° flexion) during BDE. The SEMG data were expressed as a percentage of root mean square mean values obtained in the maximal voluntary isometric contraction. Results: Greater muscle activity of the IO (p = 0.001), MF (p = 0.009), and ICLT (p = 0.021) of the raised lower limb side and the EO (p = 0.001) and MF (p = 0.009) of the contralateral side were demonstrated in the knee joint flexion position compared to the knee joint extension position. Greater local/global activity ratios of the abdominal muscle (i.e., IO and EO) of the raised lower limb (p = 0.002) and the back muscle (i.e., MF and ICLT) of the contralateral side (p = 0.028) were also noted in the knee joint flexion position. Conclusion: BDE with a knee joint flexion position might be recommended as an alternative lumbar stabilization exercise to enhance muscle activity in both the raised lower limb and the contralateral sides of the trunk for individuals with CLBP