Lincoln Center is at (39.041744, -98.146760). It has an elevation of . The city is on the north side of the Saline River. It is in the Smoky Hills region of the Great Plains. Yauger Creek, a tributary of the Saline River, goes south along the eastern edge of the city. It goes until its confluence with the Saline just south of the city. The confluence of the Saline and Lost Creek, another of the river's tributaries, is southwest of the city. It is at the intersection of Kansas Highway 14 (K-14) and Kansas Highway 18 (K-18) in north-central Kansas. Lincoln Center is northwest of Wichita, west of Kansas City, and east-southeast of Denver.