From 1983 to 1988 he was a research assistant at the Technical University of Darmstadt and the University of the Bundeswehr Munich. In 1989 he received his doctorate as Dr.-Ing. in the field of GPS/INS integration. Until the end of 1993, Prof. Eissfeller worked at Kayser-Threde GmbH Munich as project manager and head of the navigation group in the development of GPS/INS navigation systems. From 1994 to 2000 he was head of the GNSS laboratory at the University of the Bundeswehr Munich and habilitated in 1996 in the field of "Physical Geodesy and Navigation". In 2000 Prof. Eissfeller took over the professorship for Navigation.

Since 1983, the division Space of the "Institute of Space Technology and Space Applications" (ISTA), which Prof. Eissfeller heads jointly with Prof. Thomas Pany, has been active in the fields of global satellite navigation systems (GNSS), precise positioning, inertial and optical navigation and, in particular, for the European satellite navigation system Galileo. For many years now, the Institute has been in charge of the annual Munich Satellite Navigation Summit, an international conference with top-class speakers from politics, industry and science.

A significant part of the currently transmitted Galileo signal structure was developed about 10 years ago at the Institute under Prof. Günter W. Hein in cooperation with colleagues from other European institutions and is now received by more than 100 million mobile phone users. ISTA also represents the Federal Ministry of Transport and Digital Infrastructure (BMVI) in various working groups on Galileo at the European Commission in Brussels. As a German expert in a total of four working groups of the European Commission and one working group of ESA, Prof. Eissfeller will continue to serve as "Excellent Emeritus" of the University.

In July 2019, the then President of the University of the Bundeswehr Munich, Prof. Merith Niehuss, awarded Prof. Eissfeller the honorary title "Emeritus of Excellence".