During the past decade, biofuel cells (BFCs) have emerged as an emerging technology on account of their ability to directly generate electricity from biologically renewable catalysts and fuels. Due to the boost in nanotechnology, significant advances have been accomplished in BFCs. Although it is still challenging to promote the performance of BFCs, adopting nanostructured materials for BFC construction has been extensively proposed as an effective and promising strategy to achieve high energy production. In this review, we presented the major novel nanostructured materials applied for BFCs and highlighted the breakthroughs in this field. Based on different natures of the bio-catalysts and electron transfer process at the bio-electrode surfaces, the fundamentals of BFC systems, including enzymatic biofuel cells (EBFCs) and microbial fuel cells (MFCs), have been elucidated. In particular, the principle of electrode materials design has been detailed in terms of enhancing electrical communications between biological catalysts and electrodes. Furthermore, we have provided the applications of BFCs and potential challenges of this technology.