This paper introduces a methodology for the yield measurement of a neutron burst using neutron proportional counters. This methodology is to be applied when single neutron events cannot be resolved in time by nuclear standard electronics, or when a continuous current cannot be measured at the output of the counter. The methodology is based on the calibration of the counter in pulse mode, and the use of a statistical model to estimate the number of detected events from the accumulated charge resulting from the detection of the burst of neutrons. The model is developed and presented in full detail. For the measurement of fast neutron yields generated from plasma focus experiments using a moderated proportional counter, the implementation of the methodology is herein discussed. An experimental verification of the accuracy of the methodology is presented. An improvement of more than one order of magnitude in the accuracy of the detection system is obtained by using this methodology with respect to previous calibration methods.