We have tested the Monte Carlo code FLUKA for its ability to assist in the development of a better system for the in vivo measurement of fluorine. We used it to create a neutron flux map of the inside of the in vivo neutron activation analysis irradiation cavity at the McMaster Accelerator Laboratory. The cavity is used in a system that has been developed for assessment of fluorine levels in the human hand. This study was undertaken to (i) assess the FLUKA code, (ii) find the optimal hand position inside the cavity and assess the effects on precision of a hand being in a non-optimal position and (iii) to determine the best location for our γ-ray detection system within the accelerator beam hall.Simulation estimates were performed using FLUKA. Experimental measurements of the neutron flux were performed using Mn wires. The activation of the wires was measured inside (1) an empty bottle, (2) a bottle containing water, (3) a bottle covered with cadmium and (4) a dry powder-based fluorine phantom. FLUKA was used to simulate the irradiation cavity, and used to estimate the neutron flux in different positions both inside, and external to, the cavity. The experimental results were found to be consistent with the Monte Carlo simulated neutron flux. Both experiment and simulation showed that there is an optimal position in the cavity, but that the effect on the thermal flux of a hand being in a non-optimal position is less than 20%, which will result in a less than 10% effect on the measurement precision. FLUKA appears to be a code that can be useful for modeling of this type of experimental system.