Context : Aims : NGC 2264 is a young cluster with a rich circumstellar disk population which makes it an ideal target for studying the evolution of stellar clusters . Our goal is to study the star formation history of NGC 2264 and to analyse the primordial disk evolution of its members . Methods : The study presented is based on data obtained with the Infrared Array Camera ( IRAC ) and the Multiband Imaging Photometer for Spitzer ( MIPS ) on board the Spitzer Space Telescope , combined with deep near-infrared ( NIR ) ground-based FLAMINGOS imaging and previously published optical data . Results : We build NIR dust extinction maps of the molecular cloud associated with the cluster , and determine it to have a mass of 2.1 \times 10 ^ { 3 } M _ { \odot } above an A _ { \mathrm { V } } of 7 mag . Using a differential K _ { s } -band luminosity function ( KLF ) of the cluster , we estimate the size of the population of NGC 2264 , within the area observed by FLAMINGOS , to be 1436 \pm 242 members . The star formation efficiency is \geq \sim 25 % . We identify the disk population and divide it into 3 groups based on their spectral energy distribution slopes from 3.6 \mu m to 8 \mu m and on the 24 \mu m excess emission : ( i ) optically thick inner disks , ( ii ) anaemic inner disks , and ( iii ) disks with inner holes , or transition disks . We analyse the spatial distribution of these sources and find that sources with thick disks segregate into sub-clusterings , whereas sources with anaemic disks do not . Furthermore , sources with anaemic disks are found to be unembedded ( i.e. , with A _ { V } < 3 mag ) , whereas the clustered sources with thick disks are still embedded within the parental cloud . Conclusions : NGC 2264 has undergone more than one star-forming event , where the anaemic and extincted thick disk population appear to have formed in separate episodes : the sources with anaemic disks are more evolved and have had time to disperse and populate a halo of the cluster . We also find tentative evidence of triggered star-formation in the Fox Fur Nebula . In terms of disk evolution , our findings support the emerging disk evolution paradigm of two distinct evolutionary paths for primordial optically thick disks : a homologous one where the disk emission decreases uniformly at NIR and mid-infrared ( MIR ) wavelengths , and a radially differential one where the emission from the inner region of the disk decreases more rapidly than from the outer region ( forming transition disks ) .