Towns are marked in bold and market towns in italics: Babice - Bohumilice - Bohunice - Borová Lada - Bošice - Budkov - Buk - Bušanovice - Chlumany - Chroboly - Chvalovice - Čkyně - Drslavice - Dub - Dvory - Horní Vltavice - Hracholusky - Husinec - Kratušín - Křišťanov - Ktiš - Kubova Huť - Kvilda - Lažiště - Lčovice - Lenora - Lhenice - Lipovice - Lužice - Mahouš - Malovice - Mičovice - Nebahovy - Němčice - Netolice - Nicov - Nová Pec - Nové Hutě - Olšovice - Pěčnov - Prachatice - Radhostice - Stachy - Stožec - Strážný - Strunkovice nad Blanicí - Šumavské Hoštice - Svatá Maří - Těšovice - Tvrzice - Újezdec - Vacov - Vimperk - Vitějovice - Vlachovo Březí - Volary - Vrbice - Záblatí - Zábrdí - Zálezly - Zbytiny - Zdíkov - Žárovná - Želnava - Žernovice Prachatice District borders Germany in the southwest and briefly Austria in the south.

Most of the territory has a foothill character, but along the state border, the landscape is mountainous, and in the east, the terrain is only slightly undulating.

The majority of the district is located at an altitude of 600–800 m. The territory extends into three geomorphological mesoregions: Bohemian Forest Foothills (north, centre and southeast), Bohemian Forest (south and west), and České Budějovice Basin (small part in the east).

The largest body of water is the Husinec Reservoir, with an area of 61 ha (150 acres).

[3] After World War II, the German population was expelled, and the district experienced a notable demographic change as more ethnic Czechs were settled in the region.