This Research Communication describes the initial operation of a pilot-scale intermittently aerated sequencing batch reactor system, which is located at an Irish dairy processing factory. Laboratory-scale research has facilitated the design specifications and operational parameters necessary for the construction and running of a pilot-scale. Laboratory scale research was necessary prior to the pilot scale system to ensure high quality treatment and nutrient removal efficiencies. The pilot system operates with a hydraulic retention time of 4 d, a solids retention time of 16 d and a cycle length of 12 hours. There are 4 non-aeration and aeration phases within the system's react phase. This system has a 3000 l working volume, treating 375 l of wastewater per cycle, 750 l daily. The system was seeded from an aeration tank at the dairy processing factory where the unit is located. The system is operating with the goal to remove both nitrogen and phosphorus from the wastewater biologically, reducing the need for chemical treatment. Currently, the system is performing with high efficiency, treating the wastewater to an acceptable level according to the Irish Environmental Protection Agency for discharge into surrounding water bodies. Therefore, the initial removal results demonstrate this technology's suitability for the treatment of high strength dairy wastewaters.