The recent development in the miniaturisation of small satellites and their subsystems has opened a new window of research for the universities around the globe. The low-cost, lightweight, small and flexible satellites have resulted in a broad range of multi-cube format small satellites, constructed from one-to-many adjoined cubes, having total mass between 1 and 10kg. The most challenging design part of the small satellites is to implant a large number of subsystems in a limited space. In order to resolve this issue, the designers are trying to shrink down the subsystem’s dimensions further. In this paper, a magnetorquer coil is designed and analysed for a 4U (4 units cube; 33 × 33 × 16.5)cm3 and 8U (8 units cube; 33 × 33 × 33)cm3 multi-cube small satellites, respectively. The coil is embedded in the six internal layers of an eight-layers printed circuit board (PCB). The designed magnetorquer system is fully reconfigurable and multiple coils configurations can be achieved by attaching them in series, parallel and hybrid arrangements. Due to embedded nature, the heat generated by the coil may damage the components mounted on the PCB outer surfaces. Therefore, thermal analysis is performed to ensure that the coil generated heat will not cross the PCB components temperature safety limits. All the possible combinations of the coils are analysed for current drawn, power consumption, heat dissipation, magnetic moment generation and resultant torque. A desired torque can be attained by using a particular coil configuration at the cost of specific amount of consumed power and PCB surface thermals.