A fluid sample collection device for a disk-based fluid separation system is disclosed. The disk-based separation system includes a compact microfluidic disk with at least one flow channel pattern formed on a side surface of the disk. At least one orifice is formed on an outflow boundary of the disk and is designed in fluid communication with the flow channel pattern through a communication channel. The fluid sample collection device includes at least one collection tube having an open end serving as a fluid receiving end and corresponding to the orifice of the disk with a distance. When the disk is rotated, at least a portion of fluid sample in a sample processing reservoir formed on the disk is delivered by centripetal force through the communication channel and the orifice, and finally the expelling fluid sample is collected in the collection tube.