The process of carbon sequestration in soil allows to reduce human-induced impact on climate change and to improve soil quality. There are a number of agricultural techniques that are used to increase the efficiency of this process. Various methods of fast neutron activation analysis (14 MeV) are currently of particular interest for monitoring of sequestration. Author proposes a step-by-step procedure aimed on estimation of minute concentration of soil carbon. The quantitative characteristics of soil properties and composition are derived from Monte Carlo simulation with Geant4 toolkit.