5-Fluorouracil (5-FU) is a well-known cytostatic drug, which is often used in cancer treatments. Yet, it is also a very dangerous compound for people who are occupationally exposed to it for a long time, such as pharmacy employees, nurses and cleaning staff. We aimed to improve and implement a LC-MS/MS method for 5-FU quantification on surface contamination samples collected with swabs in a pharmacy department and outpatient nursing station of a university hospital. To improve the existing methods to quantify 5-FU, we compared a LC-MS/MS method using the frequently applied electrospray ionization source (ESI) with a UniSpray ionization source (USI). To determine the contamination of 5-FU in a pharmacy department preparing 5-FU infusion bags, which are then given to patients in the outpatient nursing stations, we collected multiple surface swabs of the laminar flow cabinets and frequently touched objects, before the preparation and administration of 5-FU and afterwards. Furthermore, we sampled the protective gloves and the bare hands of employees of the pharmacy department, involved in the preparation of the infusion bags. Using the USI source, we were able to reach the lowest limit of quantification (LOQ). With this technique, we were able to detect 5-FU contamination on the laminar flow cabinets and frequently used objects in the pharmacy department and the outpatient nursing station in the very low ng/cm² range. This contamination was mostly higher after preparation or administration than before. While we also found 5-FU on the protective gloves, we almost found no 5-FU on the skin of the pharmacy technicians preparing the 5-FU infusion bags. In conclusion, our method was able to detect very low concentrations of 5-FU contamination, but the contamination we found is very unlikely to result in any issues for the personnel working in these areas.