In 1982, he worked for one year as a post-doctoral fellow with the IBM Research Laboratory in San Jose, California.
After three years as an academic assistant in Hannover he became a Heisenberg fellow of the German Research Foundation (DFG – Deutsche Forschungsgemeinschaft) in 1985.
Among them are his works on the Heisenberg microscope and the measurement of the Wigner function of the quantum state of matter and light.
From 1996 to 2001, he was vice president of the German Research Foundation (DFG) where he dedicated himself to encouraging young academics.
During his term of presidency, he had to implement a series of reforms due to drastic reductions in order to downsize structures and to promote excellence.
In 2006, Mlynek was one of the co-founders of the foundation "Haus der kleinen Forscher" which was supported by the Helmholtz Association from the beginning.