Elk Creek was established around 1873 following construction of the Atchison and Nebraska Railroad through the area, taking its name from the nearby creek, itself named for elk once seen along its banks.

Elk Creek is a village with ZIP code 68348, and its population has fallen steadily — 112 (2000), 98 (2010), down to 67 at the 2020 Census. Harpsichord builder David Jacques Way (1918–1994) was a native of Elk Creek. The most distinctive current fact about the town is nearby: NioCorp Developments' Elk Creek Critical Minerals Project, a roughly $1.2 billion niobium, scandium, and rare-earth mine, broke ground on its mine portal in March 2026, aimed at reducing U.S. dependence on China for critical minerals.