[5] Lilly is located in eastern Cambria County at 40°25′30″N 78°37′14″W / 40.42500°N 78.62056°W / 40.42500; -78.62056 (40.425000, -78.620434),[6] in the valley of the Little Conemaugh River near its headwaters.

According to the United States Census Bureau, Lilly has a total area of 0.50 square miles (1.3 km2), all land.

The racial makeup of the borough was 99.47% White, 0.21% Native American, 0.11% Asian, 0.11% Pacific Islander, and 0.11% from two or more races.

Sewage treatment in Lilly is provided by the Central Mainline Sewer Authority.

A dedication ceremony was held on August 21, 2006, by local congressman John Murtha.