One of eight experts who drew up the plans for CERN, Bakker later directed the synchrocylcotron design group.
In 1951 he was invited by Professor Auger (Director of UNESCO's Department of Natural Sciences, Paris) to be one of the eight experts assigned to drawing up plans for the development of CERN. In 1952 he became Director of the group responsible for the designing and construction of the CERN Synchro-Cyclotron (SC), ultimately becoming a member of the Directorate as the Director of SC Division on a part-time basis.
He succeded Felix Bloch in September 1955, and was Director-General of CERN until April 1960. He was killed in a plane accident in April 1960. John Adams was appointed as acting Director-General for the following 15 months.