Multi channel natural circulation loops are used for various household and industrial applications like solar water heaters, thermal & nuclear power plants, etc. In the present work a computational model has been developed to investigate transient performance of a parallel channel rectangular natural circulation system with vertical heaters and horizontal common cooler. At first, mathematical modelling has been performed for a dual heater channel based natural circulation system. Thereafter, the governing equations of momentum and energy have been discretized using the schemes of finite difference and converted into a computer code. Subsequently, the transient performance of the system is assessed and sensitivity analysis of the flow in each of the channels with respect to heater power has also been studied. Finally, an attempt has been made to gain insights into a dual vertical heater channel rectangular natural circulation system with common horizontal cooler.