Objective To conduct a meta-analysis on the sensitivity and specificity of neutrophil CD64 and C-reactive protein (CRP) for diagnosing neonatal sepsis by retrieving all the relevant high quality publications, so as to provide evidences for clinicians to select diagnosis indicators. Methods The publication about the sensitivity and specificity of neutrophil CD64 and CRP for diagnosing neonatal sepsis were searched in PubMed, EMBASE and Science Citation Index Expanded from the set-up time to Oct. 15, 2013. All the trials were evaluated strictly and the included trials were analyzed by meta-analysis. The odds radio (OR) for the sensitivity and specificity of CD64 and CRP for diagnosing neonatal sepsis was calculated. Results Eight studies were included for analysis. Totally 578 cases were positive and 854 cases were negative according clinical diagnosis. Meta analysis showed that the sensitivity of CD64 for diagnosing neonatal sepsis was significantly higher than that of CRP (OR=2.79,95%CI [1.59,4.92], P=0.000 4), while the specificities of CD64 and CRP for diagnosing neonatal sepsis had no significant difference (OR=0.81,95%CI [0.50,1.30],P=0.37). Conclusion This meta-analysis shows that CD64 is more sensitive than CRP for diagnosing neonatal sepsis, but the specificities of CD64 and CRP are similar for diagnosing neonatal sepsis.