Protecting public health, taking preventive measures and ensuring recovery in case of any disease are conditions for creating a healthy life. In order to create this life, the manufacturing process of the pharmaceutical industry needs to be formed carefully. In this study there is a risk analysis application into operational processes of a pharmaceutical company. In application study, operational processes of sample company were examined and analyzed from October to May. Within the scope of the study, a two-stage approach was proposed in the analysis of the data obtained. In the first phase, fishbone analysis was carried out to determine the risks in the operational processes and the potential risks in two separate production lines were determined. In the second stage, the risk prioritization method was used and risk priority numbers (RPN) were calculated for all risks. In all these analysis, more realistic and valid results were obtained with the usage of fuzzy logic and the calculations of RPNs were made more objective and independent from analysts. After the determination of RPNs, precautions were suggested for high risky failures. Following the implementation of precautions, new RPNs were calculated for all failures. The old and the new RPNs were compared for all risky failures and all precautions were examined with their impacts on the process. As a result, all examined failures' risk prioritization numbers were reduced in the ratio between 72% and 90%, the operational processes were improved.