Sodium (Na) is an essential mineral for human health regulation and in excess has been associated with many diseases. Its storage has been found in rapidly (soft tissue) and slowly exchangeable pools (bone) in human body. However, Na concentration and metabolism information in human bone and soft tissue cannot be determined using conventional biological urine and blood samples. The aim of this study was to apply a transportable neutron generator based in vivo neutron activation analysis technique to separately quantify Na in bone and soft tissue. Two pigs were fed with low and high Na diet to investigate the effects of dietary Na intake on Na storage and metabolism. The emitted gamma rays from Na activated by thermal neutron capture reaction in pig leg were collected using a high purity germanium detector. A biokinetic model based on internal dosimetry theorem was developed to obtain the bone and soft tissue Na concentration, as well as half-life of Na retention in the two compartments. The results show that soft tissue Na concentration was significantly higher in the pig that received a high Na diet (1057.08±43.62ppmvs704.46±45.60ppm,p=0.007). In contrast, the bone sodium concentration was not affected by dietary intervention (856.45±78.48ppmvs803.30±48.98ppm,p=0.107). The developed methodology is capable of effectively measuring altered Na levels resulting from dietary Na consumption, with great potential in exploring the association between Na intake and health outcomes such as hypertension.