In order for the deployment of quantum communication technologies in a global scale, it is necessary to meet data exchange demand of various size establishments per certain time intervals and it is important to make them cost effective and feasible. In order to meet these requirements, a lot of effort has been put into increasing key rate and having optimized systems. In this study, we focus on the improvement of raw key rate in a standardized E91 QKD system without compromising its security. Our method is to optimize photon budget allocation among three types of bits used in the system for different purposes or occurred unavoidably. These three types of bits are key bits, Bell's inequality bits and discarded bits and their ratios were 25%, 50% and 25%, respectively, in the proof-of-principle experiment. On the other hand, we present 226.22% increase in raw key rate with 83%, 10% and 7% allocation of photon budget among three types of bits. These ratios are achieved by replacing 50:50 beam splitters with a 90:10 beam splitter at one communicating side and a 93:7 beam splitter at the other communicating side. Additionally, we demonstrate that the optimum beam splitting ratios can vary depending on photon budget.