Objective To investigate the expression and clinical significance of neuropeptide S receptor 1 (NPSR1) and 5-hydroxytryptamine type 4 (5-HT4) in plasma of elderly patients with functional dyspepsia (FD).Methods Ninety-six elderly patients with FD who visited our hospital from February 2020 to August 2022 were selected as the FD group, and another 80 elderly individuals undergoing health checkup in our hospital during the same period were included as the control group. The clinical data and the plasma levels of NPSR1 and 5-HT4 were compared between the FD group and the control group. Multivariable stepwise Logistic regression analysis was performed to determine factors affecting the occurrence of FD in the elderly. The receiver operating characteristic (ROC) curve was plotted to analyze the diagnostic performance of the plasma levels of NPSR1 and 5-HT4 alone and their combination for FD in the elderly.Results The body mass index (BMI), proportions of patients with fatty liver, sleep disorder, anxiety, and depression, and levels of interleukin-6 (IL-6), cholecystokinin (CCK), and somatostatin (SS) in the FD group were higher than those in the control group (P < 0.05), while the proportions of patients with regular diets and no less than 4 hours of exercise per week as well as the level of motilin (MTL) in the FD group were lower than those in the control group (P < 0.05). The plasma level of NPSR1 in the FD group was lower than that in the control group (P < 0.05), while the level of 5-HT4 in the FD group was higher than that in the control group (P < 0.05). Multivariable stepwise Logistic regression analysis showed that combined sleep disorders [O^R = 2.735 (95% CI: 1.299, 5.756) ] and higher levels of NPSR1 [O^R = 3.203 (95% CI: 1.461, 7.023) ] and 5-HT4 [O^R = 3.093 (95% CI: 1.410, 6.781)] were risk factors for the occurrence of FD in the elderly (P < 0.05). In contrast, regular diets [O^R = 0.361, (95% CI: 0.165, 0.792)] were protective factors for the occurrence of FD in the elderly (P < 0.05). The ROC curve analysis exhibited that the sensitivities of the plasma levels of NPSR1 and 5-HT4 alone and their combination in the diagnosis of FD in the elderly were 78.13% (95% CI: 68.30%, 85.66%), 75.00% (95% CI: 64.93%, 83.03%), and 73.96% (95% CI: 63.83%, 82.14%), with the specificities being 72.50% (95% CI: 61.20%, 81.61%), 81.25% (95% CI: 70.65%, 88.79%), and 95.00% (95% CI: 87.01%, 98.39%), and the areas under the ROC curves (AUCs) being 0.779 (95% CI: 0.711, 0.838), 0.784 (95% CI: 0.716, 0.843) and 0.891 (95% CI: 0.836, 0.933), respectively.Conclusions The plasma levels of NPSR1 and 5-HT4 in elderly patients with FD are significantly higher than those in healthy people, and the combination of the plasma levels of NPSR1 and 5-HT4 exhibits high diagnostic efficacy for FD in elderly patients.