A network meta-analysis evaluated the efficacy and safety of 12 Chinese patent medicines (CPM) in combination with conventional western medicine (CWM) in the treatment of functional dyspepsia (FD). It included 76 randomized controlled trials with 7575 patients from databases searched until September 2025. All combinations of CPM + CWM were more effective than CWM alone at the overall effective rate, with the best being Jinghua Weikang Capsules + CWM (RR = 1.46, 95% CI 1.28–1.67; SUCRA = 98.4%), Wuling Capsules + CWM (RR = 1.29, 95% CI 1.18–1.41; SUCRA = 80.9%) and Qizhi Weitong + CWM granules (RR = 1.26, 95% CI 1.14–1.38; SUCRA = 69.2%). For motilin levels, Wuling Capsules + CWM, Zhizhu Kuanzhong capsules + CWM, and Simo Tang oral liquid + CWM helped significantly, while for gastrin, Liuwei Nengxiao capsules + CWM, Dalitong granules + CWM, and Simo Tang + CWM. No combination of CPM + CWM increased the risk of adverse events significantly, except for Wuling Capsules + CWM versus Qizhi Weitong + CWM (OR = 4.82, 95% CI 1.02–22.87). According to CINeMA, the certainty of the evidence was low for most comparisons.