Solar Home Systems are a promising solution to enable access to affordable, reliable, sustainable, and modern energy for non-electrified areas, especially in the Global South. In this study, the influence of the charge controller technologies Maximum Point Tracker (MPPT) and Pulse Width Modulation (PWM) on the optimal system design and system performance is analyzed. Therefore, a multi-objective optimization that minimizes the number of days with Power-Cut-Offs and the Levelized Cost of Electricity for three Solar Home System sizes and three sub-saharan locations is conducted. Cost savings of the MPPT controller are in the range of 4.0% to 8.6% compared to the PWM controller. This is achieved by a reduction of the optimal installed photovoltaic peak power by 31.2% to 38.6% and the battery capacity by 2.8% to 8.8%. A sensitivity analysis shows the high robustness of cost savings regarding a variation in solar irradiance, load profile, and charge controller investment costs. Therefore, MPPT charge controllers are a promising solution even for the smallest Solar Home System sizes to reduce system costs compared to PWM controllers. The applied numerical simulation tool is open-source to enhance openness and transparency in modeling studies.