The early detection of anomalies through the analysis of the neutron noise recorded by incore and ex-core instrumentation gives the possibility to take proper actions before such problems lead to safety concerns or impact plant availability. The study of the neutron fluctuations permits to detect and differentiate anomalies depending on their type and possibly to characterize and localize such anomalies. This method is non-intrusive and does not require any external perturbation of the system. To effectively use the neutron noise for reactor diagnostics it is essential to accurately model the effects of the anomalies on the neutron field. This paper deals with the development and validation of a neutron noise simulator for reactors with different geometries. The neutron noise is obtained by solving the frequency-domain two-group neutron diffusion equation in the first order approximation. In order to solve this partial differential equation a code based on a high order finite element method is developed. The novelty of this simulator resides on the possibility of dealing with rectangular meshes in any kind of geometry, thus allowing for complex domains and any location of the perturbation. The finite element method also permits automatic refinements in the cell size (h-adaptability) and in its polynomial degree (p-adaptability) that lead to a fast convergence. In order to show the possibilities of the neutron noise simulator developed a perturbation in a hexagonal two-dimensional reactor is investigated in this paper.