Nano-electro-mechanical systems (NEMS) require perforated beams for structural integrity. Hole sizes, hole numbers, and scale effects need to be modelled appropriately in their design. This paper presents a new finite element model to investigate the modal behaviour of longitudinally perforated nanobeams (LPNBs) using the classical Euler–Bernoulli beam theory. A symmetric array of holes arranged parallel to the length direction of the beam with equal spacing was assumed for the perforation. The non-local Eringen’s differential form was used to incorporate the nanoscale sizes. The accuracy of the proposed model was verified by comparing the obtained results with the available analytical solutions for fully filled nanobeams. The effects of aspect ratios, non-local parameters, boundary conditions, and perforation characteristics on the modal behaviour of LPNBs were investigated. The non-local parameter reduced the natural frequency owing to a decrease in the stiffness of the structures. However, the perforation filling ratio led to higher values of the fundamental frequency. Furthermore, compared with other boundary conditions, clamped–clamped boundary conditions demonstrated the best performance in terms of the maximum frequency.