The Balloon-borne Investigation of Temperature and Speed of Electrons in the corona (BITSE) mission, performed by KASI and NASA, used a high-altitude scientific balloon. The purpose of BITSE was to investigate the scientific feasibility of electron temperature and velocity measurements in the solar corona using wavelength-dependent polarization brightness differences. KASI was responsible for developing the command and data handling (C&DH) system, including the main electronics unit and flight software (FSW). Here, we introduce the development of C&DH system of BITSE and describe the ground integration and test and flight operations. The main electronics unit was built using an industrial-grade modular system in customized enclosures that withstood the operating environment. The FSW was developed using the core Flight System (cFS), an open-source software framework developed by NASA and used in several successful space missions. BITSE was launched at Fort Sumner, New Mexico, USA, on September 18, 2019. It observed the solar corona for approximately 4 hours at an altitude of approximately 40 km and collected 16,000 solar corona images. This study could provide guidelines for developing the C&DH system for future balloon missions.