Disclosed is an apparatus for separating a desired radionuclide. The apparatus includes a fluid supply part that supplies a fluid including a sample containing the radionuclide or a reagent, a column separation part that receives the fluid supplied from the fluid supply part and separate the radionuclide, and including a driving member passage, through which the fluid, from which the radionuclide has been separated, is discharged, a fluid recovery part including a plurality of recovery containers that recover the fluid discharged through the column separation part, a sensor that senses the fluid in the column separation part, and a controller that controls driving of the fluid supply part, the column separation part, and the fluid recovery part such that, after residual fluid remaining in an interior of the driving member passage is recovered into the recovery container, the recovery container located at a recovery position is replaced.