An automated microarray processing system includes a microarray housing assembly module, an incubation module, a washing module and at least one automated transport module. With the automated transport module being mechanically moved among the microarray housing assembly module, the incubation module and the washing module, biochemical reaction of a reaction region of a microarray and a biological sample solution disposed therebetween is automatically performed, and the reacted microarray is automatically cleaned when the biochemical reaction of the microarray is completed.