Neonatal pneumonia is a serious respiratory infectious disease with a high rate of case fatality in developing countries. Salivary cytokines could serve as interesting noninvasive markers in the diagnosis of neonatal pneumonia. The aim was to assess the diagnostic role of salivary and serum interleukin‐6 (IL‐6), C‐reactive protein/mean platelet volume (CRP/MPV) ratio, and the combination of these markers in the diagnosis of late‐onset neonatal pneumonia in full‐term neonates. Seventy full‐term neonates, 35 with late‐onset neonatal pneumonia and 35 controls, were enrolled in this prospective case‐control study. Complete blood count (CBC), salivary and serum IL‐6, and CRP concentrations were measured for all the study subjects. The sensitivity, specificity, positive predictive value, and negative predictive value of salivary IL‐6, serum IL‐6, and CRP/MPV ratio for the diagnosis of late‐onset neonatal pneumonia were determined. At the cutoff point of >34 pg/ml, salivary IL‐6 showed 82.86% sensitivity and 91.43% specificity. CRP/MPV ratio showed a sensitivity of 97.14% and specificity of 85.71% at a cutoff value > 0.88. The combination of salivary IL‐6 and CRP/MPV ratio improved the sensitivity and specificity to 100%. The current study shows for the first time that both salivary IL‐6 and CRP/MPV ratio are suitable markers for the diagnosis of late‐onset neonatal pneumonia in full‐term neonates.