The balloon-borne cosmic-ray experiment CREAM (Cosmic Ray Energetics And Mass) has completed two flights in Antarctica, with a combined duration of 70 days. One of the detectors in the payload is the SCD (silicon charge detector) that measures the charge of high energy cosmic rays. The SCD was assembled with silicon sensors. A sensor is a 4 × 4 array of DC-coupled PIN diode pixels with the total active area of 21 × 16 mm2. The SCD used during the first flight (December 2004-January 2005) was a single layer device, then upgraded to a dual layer device for the second flight (December 2005-January 2006), covering the total sensitive area of 779 × 795 mm2. Flight data demonstrated that adding a second layer improved SCD performance, showing excellent particle charge resolution. With a total dissipation of 136 W for the dual layer system, special care was needed in designing thermal paths to keep the detector temperature within its operational range. As a consequence, flight temperatures of the SCD, even at diurnal maximum were kept below 38°C. The SCD mechanical structure was designed to minimize the possibility of damage to the sensors and electronics from the impacts of parachute deployment and landing. The detector was recovered successfully following the flight and is being refurbished for the next flight in 2007. Details of construction, operation, and performance are presented for the dual-layered SCD flown for the second CREAM flight.