The Sanbao Mn–Ag (Zn-Pb) deposit located in the Laojunshan ore district is one of the most important deposits that has produced most Ag and Mn metals in southeastern Yunnan Province, China. Few studies are available concerning the distribution and mineralization of Ag, restricting further resource exploration. In this study, detailed mineralogy, chronology, and geochemistry are examined with the aim of revealing Ag occurrence and its associated primary base-metal and supergene mineralization. Results show that manganite and romanèchite are the major Ag-bearing minerals. Cassiterite from the Mn–Ag ores yielded a U–Pb age of 436 ± 17 Ma, consistent with the Caledonian age of the Nanwenhe granitic pluton. Combined with other geochemical proxies (Zn-Pb-Cu-Sn), the Sanbao Mn–Ag deposit may originally be of magmatic hydrothermal origin, rather than sedimentary. The Ag-rich (Zn-Pb (Sn)-bearing) ore-forming fluids generated during the intrusion of the granite flowed through fractures and overprinted the earlier Mn mineralization. Secondary Ag (and possibly other base-metals) enrichment occurred through later supergene weathering and oxidation.