This two volume set LNCS 8634 and LNCS 8635 constitutes the refereed conference proceedings of the 39th International Symposium on Mathematical Foundations of Computer Science, MFCS 2014, held in Budapest, Hungary, in August 2014. The 95 revised full papers presented together with 6 invited talks were carefully selected from 270 submissions. The focus of the conference was on following topics: Logic, Semantics, Automata, Theory of Programming, Algorithms, Complexity, Parallel and Distributed Computing, Quantum Computing, Automata, Grammars and Formal Languages, Combinatorics on Words, Trees and Games.