The diagnostic utility of F-18 fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) compared to bone marrow biopsy (BMB) in patients with non-Hodgkin lymphoma (NHL) remained to be confirmed. This study aimed to compare BMB and PET/CT for bone marrow infiltration (BMI) in patients with NHL. PubMed, Embase, and the Cochrane library were searched for papers published up to October 2021. The outcomes were the true positive and negative and false positive and negative rates for BMB and PET/CT. The summarized sensitivity, specificity, positive likelihood ratios (PLR), negative likelihood ratios (NLR), and diagnostic odds ratios (DOR) were calculated. Thirteen studies with a total of 2396 patients were included. Significant differences are observed between BMB and PET/CT for sensitivity (relative ratio: 0.749; 95% CI: 0.586-0.956; P=0.020) and NLR (relative ratio: 1.839; 95% CI: 1.106-3.058; P=0.019), but not for specificity (P=0.819), PLR (P=0.802), and DOR (P=0.150). The summary area under the receiver operating characteristic curves for BMB is 0.692 (SE: 0.170) and 0.977 (SE: 0.021) for PET/CT. PET/CT presents a better sensitivity and NLR for the detection of BMI in patients with NHL, whereas no differences are found regarding specificity, PLR, and DOR compared with BMB.