After the Velvet Revolution in 1989, Šmahel was head of the Historical Institute of the Czech Academy of Sciences for eight years. Together with Petr Sommer, he initiated the foundation of the Centre for Medieval Studies in Prague and he became its first director in 1998–2004. In 1996, Šmahel was awarded the Hans Sigrist Prize. František Šmahel is a member of many prestigious scholarly associations and is the recipient of a number of foreign and Czech honours, including the ''Česká hlava'' National Prize for Science (2013).