The Jan Kluyver-prijs for the best English summary of a Nikhef PhD thesis was established in 2010 by the Education Committee of the Research School for Subatomic Physics. The jury consists of the former directors of Nikhef. 

Without the effort of prof. dr. Jan Kluyver the Nikhef collaboration in 1975 wouldn't have been possible. Because the key output of Nikhef is undoubtedly the excellent education of the physicists that earn their PhDs at Nikhef, and because they partly determine Nikhef's future research fields, the prize carries the name of Jan Kluyver.

In 2011 the Jan Kluyver prize was awarded to Gideon Koekoek and Alexander Doxiadis.
In 2010 the Jan Kluyver was awarded to Tristan de Pree.