Elxleben is located on the Wipfra river around ten kilometers north-east of Arnstadt. The Thuringian state capital of Erfurt is around ten kilometers north of the municipality. Elxleben belongs to the Riechheimer Berg administrative community. The administrative seat is located in the municipality of Osthausen-Wülfershausen. Elxleben borders on the municipalities of Amt Wachsenburg, Elleben and Alkersleben.