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Abstract Background Chronic nonbacterial osteomyelitis (CNO) is a rare chronic autoinflammatory syndrome affecting mainly children and young adults. The natural history of the disease is marked by recurrent pain as the mainstay of inflammatory outbreaks. Typical radiographic findings are osteosclerosis and hyperostosis of the medial clavicle, sternum and first rib. Compression of the brachial plexus is exceedingly rare and one of the few surgical indications. Literature on total clavicle reconstruction is scarce. While claviclectomy alone has been associated with fair functional and cosmetic outcomes, several reconstruction techniques with autograft, allograft or even cement (“Oklahoma prosthesis”) have been reported with the aim of achieving better pain control, cosmetic outcome and protecting the brachial plexus and subclavian vessels. We herewith report a unique case of complicated CNO of the clavicle treated with total clavicle reconstruction using a free peroneal graft. Case presentation A 21-year-old female patient presented with CNO of her left clavicle, associated with recurrent, progressive and debilitating pain as well as limited range of motion. In recent years, she started complaining of paresthesia, weakness and pain radiating to her left arm during arm abduction. The clavicle diameter reached 6 cm on computed tomography, with direct compression of the brachial plexus and subclavian vessels. Following surgical biopsy for diagnosis confirmation, she further developed a chronic cutaneous fistula. Therefore, a two-stage total clavicle reconstruction using a vascularized peroneal graft stabilized by ligamentous reconstruction was performed. At two-year follow-up, complete pain relief and improvement of her left shoulder Constant-Murley score were observed, along with satisfactory cosmetic outcome. Conclusions This case illustrates a rarely described complication of CNO with direct compression of the brachial plexus and subclavian vessels, and chronic cutaneous fistula. To our knowledge, there is no consensus regarding the optimal management of this rare condition in this context. Advantages and complications of clavicle reconstruction should be carefully discussed with patients due to limited evidence of superior clinical outcome and potential local and donor-site complications. While in our case the outcomes met the patient’s satisfaction, it remains an isolated case and further reports are awaited to help surgeons and patients in their decision process.