Mechanistic questions regarding kidney stone formation have led researchers to look for the presence of trace elements. Neutron activation analysis is able to identify elements at parts-per-million concentrations. Four different types of kidney stones were irradiated with thermal neutrons to produce radioisotopes. Gamma spectroscopy of samples at different counting times was used to reduce identification errors by correlating results with the half-life of identified elements. For more precise identification, Monte Carlo simulation was used to cross-check the identification process. The simulation showed promising results that could lead to fast and accurate identification of trace elements as the simulation code is improved. Sodium (Na), potassium (K), calcium (Ca), bromine (Br), samarium (Sm), zinc (Zn), cadmium (Cd), ytterbium (Yb), gold (Au), cobalt (Co), and manganese (Mn) were identified as being present in the stones, by both the experimentally measured gamma spectrum and the simulation. Among these, Ca, Br, and Zn were found to be of potential clinical relevance via a literature review. Concentrations of the elements were compared to those noted in the literature. For uric acid stones, a correlation with the literature was found for Zn and Ca. A negative correlation was found between Zn and Br for non-uric acid stones. More samples are needed to test for statistical significance.