In this paper, the problem of controlling parallel charging system with supercapacitors for electric vehicle applications is considered. When the vehicle parks at the station, the charging process of supercapacitors needs to be completed in less than 30 seconds. The control objective is then to tightly regulate the supercapacitors state of charge (SOC) to a given reference constant and to ensure an adequate current sharing between different parallel chargers. Indeed, the current sharing is a critical issue for parallel charging system with supercapacitors, which is a nonlinear system with control inputs constraints. Besides, the SOC depends on the supercapacitors internal voltage, which is not accessible for measurement. Therefore, based on a large‐signal model of the parallel‐chargers‐supercapacitors system, an output feedback controller (combining a state observer and a nonlinear control laws) is designed. The controller is formally shown to meet all objectives, namely, closed‐loop stability, SOC reference tracking, and equal current sharing. The effectiveness of the proposed output feedback controller approach is verified both by simulation and by experimental tests.