Merklingen is located on the plateau of the Swabian Jura, about 20 kilometers northwest of Ulm, between Geislingen and Blaubeuren.

The neighboring communities of Merklingen are (clockwise from north): Nellingen, Dornstadt, Laichingen (all Alb-Donau-Kreis), Hohenstadt, Drackenstein, Bad Ditzenbach (all Göppingen district).

Merklingen, consisting of the main town and the hamlet Widderstall, remained an independent municipality with its own administration.

Merklingen came in 1810 to the Kingdom of Württemberg and was allocated to Oberamt Blaubeuren, which became in 1938 the district of Ulm.

In the neighboring village of Nellingen a high school is established, Realschule and Gymnasium can be visited in Laichingen.