A three-dimensional computational model for air-breathing microfluidic fuel cells (AMFCs) with flow-over and flow-through anodes is developed. The coupled multiphysics phenomena of fluid flow, species transport and electrochemical reactions are resolved numerically. The model has been validated against experimental data using an in-house AMFC prototype with a flow-through anode. Characteristics of fuel transfer and fuel crossover for both types of anodes are investigated. The model results reveal that the fuel transport to the flow-over anode is intrinsically limited by the fuel concentration boundary layer. Conversely, fuel transport for the flow-through anode is convectively enhanced by the permeate flow, and no concentration boundary layer is observed. An unexpected additional advantage of the flow-through anode configuration is lower parasitic (crossover) current density than the flow-over case at practical low flow rates. Cell performance of the flow-through case is found to be limited by reaction kinetics. The present model provides insights into the fuel transport and fuel crossover in air-breathing microfluidic fuel cells and provides guidance for further design and operation optimization. (C) 2014 Elsevier B.V. All rights reserved.