Stefan Kubik studied chemistry at Heinrich Heine University Düsseldorf and King's College London. He graduated in 1988 with a diploma thesis under the supervision of Prof. Dr. G. Wulff and received his Ph.D. in 1992 for work carried out within the same research group about structural aspects of amylose complexes. In 1993, he received a NATO fellowship for a postdoctoral stay in the group of Prof. J. Rebek Jr. at MIT, where he studied self-replicating and self-assembling systems.

After returning to Düsseldorf in September 1994, he began investigating the host-guest chemistry of cyclopeptides containing non-natural aromatic amino acid subunits. This work led to his habilitation in April 2002.

From March 2003 to October 2004, he was a substitute professor at the University of Wuppertal. Since November 2004, he has been a full professor at the University of Kaiserslautern (RPTU Kaiserslautern-Landau since January 2023). In 2012, he was an invited professor at the University of Burgundy in Dijon.

He has authored over 1,000 entries for the chemistry encyclopedia Römpp Online. He was guest editor of the online themed collection of Organic & Biomolecular Chemistry on Supramolecular Chemistry in Water and edited a monograph entitled "Supramolecular Chemistry in Water". He is also associate editor of the Journal of Inclusion Phenomena and Macrocyclic Chemistry.

His textbook Supramolecular Chemistry – From Concepts to Applications was published at the end of 2020 and won the 2022 Literature Prize of the Fonds der Chemischen Industrie. The second edition was published in 2024.