The Ultra-Large Scale Software (ULSS) system is a novel generation of software systems that requires to be managed and developed across multiple organizations. Such a system challenges the existing agile methods and scaled agile methods as they address only the intra-organizational cooperation. In fact, for inter-organizational coordinations, the ULSS systems have to be regulated as a city rather than being engineered as a building. This paper provides the first Framework for Agile Regulated Ultra-Large-Scale Software System (FARUL3S) that intends to regulate the ULSS systems by constraining the design spaces’ exploration. To this end, we introduced the System Design Rules Hierarchy (SDRH) as a hierarchy of dominance relations that covers the system, platform and application levels. The SDRH, which is the main artifact of our framework, ensures a distributed design spaces’ exploration and helps to provide the interoperability between the different component parts of the ULSS system. The NOV-based analysis of two case studies from the Smart City System prove that the ULSS system regulation improves the added value over its engineering. Thus, to conclude, regulating the ULSS systems makes the system more than the sum of its elements.