Clayton is in northern Johnston County, with a small portion extending northwest along US 70 Business into Wake County. In 2006, construction began on the Highway 70 Clayton Bypass, a 10.5-mile (16.9 km) stretch from Interstate 40 along the southern portion of Clayton to Highway 70 business southeast of town. It was completed in June 2008. US 70 leads southeast 13 miles (21 km) to Interstate 95 at Smithfield. Downtown Raleigh is 16 miles (26 km) northwest of Clayton via US 70 Business and Interstate 40.
According to the U.S. Census Bureau, as of the 2010 census Clayton had an area of 13.53 square miles (35.05 km2), of which 13.51 square miles (34.99 km2) were land and 0.02 square miles (0.06 km2), or 0.16%, were water. The town is part of the Neuse River watershed. The town limits now extend northeast to the Neuse River and beyond.
Town Hall is located at 111 East Second Street and is shared with The Clayton Center, a performing arts and conference center.