After completing his PhD, Philipp Kukura moved to Zürich. There he worked at the Swiss Federal Institute of Technology as a postdoctoral research assistant under the supervision of Professor Vahid Sandoghdar on nano-optics until 2010. He returned to Oxford in 2010 to work initially as an EPSRC Career Acceleration Fellow. In 2011 he was elected to a tutorial fellowship at Exeter College. In 2016 he was promoted to Full Professor of Chemistry.  
In 2018 Philipp Kukura founded Refeyn Ltd. together with Justin Benesch, Daniel Cole, and Gavin Young to commercialise mass photometry.