Environmental regulations instigated the technological and procedural revolution in shipping. One of the challenges has been sulfur emission control areas (SECA) and requirement of fuel changeover. Initially, many reports anticipated that new grades of low sulfur fuels might increase various technical problems in ship operation. This research develops a simple and easy to use method of the failure severity and intensity assessment in relation to fuel changeover. The scale of failure rate in the ship’s fuel system was evaluated qualitatively and quantitively, using developed failure frequency indicator and the time between failure. Based on 77 records of fuel system failures collected on seven ships, it has been found that frequency of failures related to SECA fuel changeover is on average nearly three times higher compared to the rest of sailing time. Their severity did not significantly change, but the structure of failures changed considerably. The method and presented results may help in improvement of ship’s systems design and on-board operational procedures.