Devices for high throughput cell electroporation include a trapping component that at least partially defines an upper boundary of a microfluidic chamber. A cell trap array is patterned on the underside of the trapping component, and a channeling component is positioned beneath the trapping component. The channeling component includes a vertically oriented nanochannel array. The trapping component and the channeling component are positioned such that a given nanochannels is positioned beneath a cell trap. During use, fluid flow holds trapped cells in secure contact with the nanochannels beneath the cell trap. The device further includes upper and lower electrode layers for generating an electric field to electroporate trapped cells via the nanochannel array. A reservoir positioned beneath the channeling component can be filled transfection reagent solution. During electroporation, the transfection reagent solution travels through the nanochannel array during to transfect the trapped cells.