To isolate the negative impacts of pulsed power loads (PPL) in a shipboard power system (SPS), energy storage systems (ESS) are usually equipped for online ESS charging and offline ESS discharging for PPL deployment. In order to achieve fast and smooth ESS charging, the generation control and ESS charging control need to be well coordinated. In addition, control constraints, such as generation and charging current bounds and ramp rates, and changes of operating conditions during charging, should also be properly considered. To better solve this important but insufficiently investigated problem, two control algorithms are presented in this paper. The first PI-based control algorithm is designed based on analysis of the desired performance and rules for coordination. The second feedback linearization based control algorithm is designed based on a simplified SPS model and ramp rates difference of supply and demand. The algorithms are simple to implement and can effectively reduce the negative impacts during supercapacitor charging. The algorithms are tested with detailed single-generator and multiple-generator SPS models. Power hardware-in-the-loop and real-time digital simulation studies are performed to demonstrate the effectiveness of the proposed algorithms.