This paper provides a Systems Engineering (SE) perspective on establishment of Single Window (SW) systems, highlighting the value of SE both on a Master Plan level for SW programmes and on an implementation level of the constituent systems. The author proposes that 1). in SW Master Plan stage, SE thinking could guide vision and capability alignment and project prioritization; 2). in implementation of the sub‐systems, SE technical processes should be promoted to ensure successful delivery of SW systems. The paper presents a study on Maritime Single Window (MSW) systems, with a review on the domain conventions and a case of an MSW initialization project. Further, the paper revisits the evolution of the Singapore MSW and the national SW Programme, and discusses agility and open‐source co‐development for future SW implementations. Additionally, the author recommends federation approach in SW implementations as preferable to integration approach as the current industry practice.