In recent decades, due to reduction in precipitation, groundwater resource management has become one of the most important issues considered to prevent loss of water. Many solutions are concerned with the investigation of groundwater flow behavior. In this regard, development of meshless methods for solving the groundwater flow system equations in both complex and simple aquifers' geometry make them useful tools for such investigations. The independency of these methods to meshing and remeshing, as well as its capability in both reducing the computation requirement and presenting accurate results, make them receive more attention than other numerical methods. In this study, meshless local Petrov–Galerkin (MLPG) is used to simulate groundwater flow in Birjand unconfined aquifer located in Iran in a transient state for 1 year with a monthly time step. Moving least squares and cubic spline are employed as approximation and weight functions respectively and the simulated head from MLPG is compared to the observation results and finite difference solutions. The results clearly reveal the capability and accuracy of MLPG in groundwater simulation as the acquired root mean square error is 0.757. Also, with using this method there is no need to change the geometry of aquifer in order to construct shape function.