Ondansetron (OND) is a serotonin type 3 receptor antagonist that exhibits antiemetic activity. From the clinical point of view, vomiting and nausea prevention is an important task. Anticancer treatment and recovery impact the patient’s overall state by affecting appetite, well-being, and physical activity, and consequently, nutrition quality. Depending on the patient’s indication and condition, parenteral nutrition is administered to meet full nutritional requirements. In addition, antiemetic drugs can be added to the parenteral nutrition (PN) admixture to treat chemo- or radio-therapy-induced nausea and vomiting. However, adding any medication to the PN admixture can result in the instability of the composition in the overall admixture. This study aimed to develop the HPLC method of determination of OND in Lipoflex special, one of the most popular, ready-to-use PN admixtures. The proposed HPLC method and the sample preparation procedure were suitable for analyzing OND in PN admixture stored under various conditions, such as exposure to sunlight and temperature. It was found that the decomposition of OND during the seven-day storage did not exceed 5% and did not depend on external factors. Based on the conducted research, it is recommended to add OND to Lipoflex special, and it is possible to store such an admixture for seven days.