Hannigan started working in Dublin where he worked for Digital Equipment. His job at the Irish company involved writing terminal server and routing codes. When he relocated to the U.S., he joined Motorola and Wellfleet Communications. He also worked for Forrester Research from 1996 to 2000 as Director of network research and implemented successful practices in the areas of enterprise networks, security technology, and product management. Hannigan was, however, known for founding the startup Q1 Labs, which was acquired by IBM in 2011. The company, which he co-founded with Sandy Bird, provided security software that can analyze and monitor events. In an interview, he said, "Our ideas are based on the simple realization that the perimeter protection paradigm that companies have relied on doesn't work in a world where the bad actors are so sophisticated. Built upon a foundation of intelligence, we must bring security closer to the data, person, and transaction.” Q1 Labs' security features were seen as compatible with IBM's analytic capability, hence the acquisition. When IBM acquired Q1 Labs, the company created a new division that focused on helping clients address security challenges. Q1 Labs formed the basis of this security division and Hannigan was tapped to lead it. According to Gartner, that division has established itself as the third largest security software company, and IDC lists Hannigan's group as a world leader in security services. IBM would later acquire startups that reinforced the division's range of security services. Hannigan retired from IBM in 2016 after four years working for the company.
Startup ventures
In November 2016, Hannigan joined Polaris Partners as a venture partner and was involved in identifying tech startups for funding and founding. As with his experience at IBM, he also focuses on cloud infrastructure and cybersecurity. Hannigan maintains that the business world is shifting from the traditional data center towards multiple cloud services. In 2019, he co-founded , a startup that offers organizations better data security across multicloud deployments through a software-as-a-service product offering. Aside from being an investor, he also serves as the CEO of the startup, which was able to raise $18.5 million after going public.