The present invention discloses an apparatus for controlling an operation of a reciprocating compressor and a method therefor which can reduce errors in an operation of a stroke estimated value of the reciprocating compressor, by previously preventing over-saturation of a magnetic flux density generated in a coil of a motor. The apparatus for controlling the operation of the reciprocating compressor includes a magnetic flux saturation constant operation unit for operating a magnetic flux saturation constant of a motor of the reciprocating compressor on the basis of a stroke estimated value of the reciprocating compressor, a stroke reference value generation unit for generating an increased or decreased stroke reference value by increasing or decreasing a predetermined stroke reference value on the basis of the magnetic flux saturation constant, and a control unit for controlling a voltage applied to the motor of the reciprocating compressor on the basis of the generated stroke reference value.