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Abstract Objectives Obstructive sleep apnea (OSA) is one of the most common chronic diseases. Trefoil factor family 3 (TFF3) peptides are secreted by major and minor salivary glands and may be involved in the pathogenesis of OSA. This study aimed to evaluate salivary TFF3 and flow rate between those with and without OSA. Material and methods This was a prospective experimental study that enrolled patients with OSA and non‐OSA. Total unstimulated saliva was collected, the salivary flow rate was measured, and the TFF3 level was analyzed by using a modified sandwich enzyme‐linked immunosorbent assay. Baseline characteristics, TFF3 level, and salivary flow rate were compared between both groups. Factors associated with the TFF3 level and flow rate were computed by using multivariate linear regression analysis. Results Twenty‐eight participants were recruited in the study: 20 patients with OSA (71.42%) and 8 non‐OSA as control. The TFF3 and salivary flow rates between both groups of non‐OSA versus OSA were comparable (TFF3 non‐OSA 61.06 vs. OSA 96.00 ng/mg; p = .276 and flow rate non‐OSA 0.40 vs. OSA 0.35 mL/min; p = .320). Factors associated with the TFF3 level were neck circumference with a negative coefficient of −16.419 (p = .042). For the salivary flow rate, only age was a significant factor with the coefficient of −0.013 (p = .044). Conclusions TFF3 and salivary flow rate were comparable between patients with OSA and non‐OSA. The factor associated with TFF3 level was neck circumference, while age was negatively associated with the salivary flow rate in patients with OSA.