Background Flexion contracture in the lower extremity is a common finding in the patient with neuromusculoskeletal disorders. However, severe cases due to prolonged immobilization in knee–chest position are rarely established and remain underreported. This condition is associated with high morbidity and reduced quality of life, especially when it comes to neglected cases with missed injury and late presentation for adequate primary care and rehabilitative program. It remains a difficult challenge to treat, with no established treatment protocol. In addition, other factors related to psychological and socioeconomic conditions may interfere and aggravate the health state of such patients. Case presentation A 19-year-old Javanese man presented with flexion contracture of bilateral hip, knee, and ankle joints due to prolonged immobilization in knee–chest position for almost 2 years following a traffic accident and falling in the bathroom. The condition had persisted for the last 3 years due to irrecoverable condition and lack of awareness. In addition, the patient also presented with paraplegia at level L2–S1, dermatitis neglecta, multiple pressure ulcers, community-acquired pneumonia, and severe malnutrition. Prolonged and sustained passive stretching with serial plastering were performed in the patient. By the time of discharge, patient was able to move and ambulate using wheelchair. Progressive improvement of range of motion and good sitting balance were observed by 3-month follow-up. Conclusion A combination of surgery and rehabilitative care is required in the setting of severe flexion contracture. Passive prolonged stretching showed a better outcome and efficacy in the management of flexion contracture, whether the patient undergoes surgery or not. However, evaluation of residual muscle strength, changes in bone density and characteristic, and the patient’s general and comorbid conditions must always be considered when determining the best treatment of choice for each patient to achieve good outcome and result. A holistic approach with comprehensive assessment is important when treating such patients.