The study of calcium diffusion in neuron cells has gained interest among research workers during the last two decades, due to its wide variety of roles in human body like muscle contraction, secretion, metabolism, signal transduction etc. Na[Formula: see text] is the first ion that comes in the hierarchy of ions affecting cytosolic Ca[Formula: see text] concentration. This Na[Formula: see text] ion helps in intracellular Ca[Formula: see text] regulation in cytosol via Na[Formula: see text]/Ca[Formula: see text] exchanger protein (NCX protein). Most of the theoretical investigations on calcium diffusion in neuron cells have been carried out for one and two dimensional cases by various research workers and that too by incorporating a point source of influx. In order to have more realistic study the more details of geometry, microstructure and physiological parameters need to be incorporated in the models. In view of above a three dimensional unsteady state model of Calcium dynamics in a neuron cell has been developed. Apart from the point source, the line and surface sources of an influx of Ca[Formula: see text]as well as the Na[Formula: see text]/Ca[Formula: see text] exchanger, have been incorporated in the model. Appropriate initial and boundary conditions have been framed. The region is discretized using three dimensional circular sectoral elements. Variational finite element method has been employed to obtain the solution. The numerical results have been computed to study effect of Na[Formula: see text]/Ca[Formula: see text] exchanger, point source, line source and surface source of an influx on Ca[Formula: see text] distribution in a neuron cell.