Martijn Finken studied both Medicine and Biomedical Sciences at Leiden University. He obtained both master degrees in 1998 and his medical degree in 2000 (cum laude). In 2001 he was awarded an NWO/AGIKO stipend, which allowed him to combine his PhD with his training in paediatrics at the Leiden University Medical Center (promotors: Prof.dr. J.M. Wit and Prof.dr. J.A. Romijn). This stipend resulted in a thesis, entitled "Preterm birth, early growth and adult metabolic health", that was defended in 2007 (cum laude). After being registered as a paediatrician in 2009, Martijn proceeded with a fellowship in paediatric endocrinology at the VU University Medical Center, which he completed in 2012.

As a paediatric endocrinologist, Martijn specialized in neonatal endocrinology. His research focuses on the long-term impact on development of abberrations in hormonal systems, in paricular the hypothalamus-pituitary-adrenal axis, in early life. He is co-promotor of 4 PhD students working on this topic. In addition to his clinical and scientific work, Martijn is vice-charmain of the institutional review board and chairman of the biobank review committee of location VUmc.