The neutron activation system at JET is a pneumatic transfer system capable of positioning activation samples close to the plasma. Its primary purpose is to provide a calibration for the time-dependent neutron yield monitors (fission chambers and solid state detectors). Various activation reactions with different high energy thresholds were used including Fe56(n,p) Mn56, Al27(n,α) 24Na, 93Nb(n,2n) 92mNb, and Si28(n,p) 28Al reactions. The silicon reaction, with its short half life (2.25 min), provides a prompt determination of the 14 MeV DT yield. The neutron induced γ-ray activity of the Si samples was measured using three sodium iodide scintillators, while two high purity germanium detectors were used for other foils. It was necessary to use a range of sample masses and different counting geometries in order to cover the wide range of neutron yields (1015–1019 neutrons) while avoiding excessive count rates in the detectors. The absolute full energy peak efficiency calibration of the detectors was measured taking into account the source-detector geometry, the self-attenuation of the samples and cross-talk effects. An error analysis of the neutron yield measurement was performed including uncertainties in efficiency calibration, neutron transport calculations, cross sections, and counting statistics. Cross calibrations between the different irradiation ends were carried out in DD and DT (with 1% and 10% tritium content) discharges. The effect of the plasma vertical displacement was also experimentally studied. An agreement within 10% was found between the 14 MeV neutron yields measured from Si, Fe, Al, Nb samples in DT discharges.