Background Lung cancer is the leading cause of cancer-related deaths worldwide, causing more than 1.6 million deaths annually, including 26,500 deaths in Brazil in 2015. The diagnosis of lung cancer in the early stages remains a challenge. Imaging tests are important for diagnostic suspicion and risk evaluation, but biopsy is needed to confirm malignancy. Minimally invasive methods for biopsy used include computed tomography-guided percutaneous biopsy (CTGB) and bronchoscopy transbronchial biopsy. The method of choice should have the best accuracy and the lowest complication rate. This systematic review is designed to map, critically evaluate and compare the effects (benefits and risks) of all lung nodule biopsy techniques.Methods We will conduct a systematic review according to the Cochrane Handbook for Systematic Reviews of Interventions recommendations.Discussion This study aims to compare the diagnostic yield and the safety of different techniques used for pulmonary nodule biopsy. We will include randomized clinical trials comparing tomography-guided percutaneous biopsy, nonguided transbronchial biopsy, fluoroscopy-guided transbronchial biopsy, transbronchial biopsy guided by endobronchial ultrasound with a radial probe and transbronchial biopsy guided by electromagnetic navigation. This study was approved by the research ethics committee of Universidade Federal de São Paulo (UNIFESP) (number 1344040918). The results of the completed protocol will be presented at any appropriate conference by the authors.Systematic review registration The protocol for this review was prospectively registered in the PROSPERO database (CRD42018092367).