Upon his return he headed the East Germany Army's Cosmonaut Training Center near Moscow until German unification in 1990, when he left the East German military with the rank of major general. Jähn was awarded the title Hero of the Soviet Union on 3 September 1978. In 1983 he received a doctorate at the Zentralinstitut für Physik der Erde in Potsdam, specialising in remote sensing of the earth. He was instrumental in forming the Association of Space Explorers. He was a founding member in 1985 and served for several years on its Executive Committee.
Starting in 1990, after Germany was reunited, he worked as a freelance consultant for the German Aerospace Center and from 1993 also for the European Space Agency (ESA) to prepare for the Euromir missions. He retired in 2002. In 2011, on the 50th anniversary of the first manned space flight by Yuri Gagarin, he explained to Der Spiegel that his taking a toy figure on his flight was not a personal choice. He took a Sandmännchen, an animated character featured on an East German children's television show, in order to film material for the show. Because he and fellow cosmonaut Vladimir Kovalyonok joked about Sandmännchen marrying another toy figure of the Russia mascot Masha, authorities found the material unsuitable for the public.