He was originally appointed last month on a three month term.
The announcement was made on Friday as institute members gathered for the organisation's annual general meeting, continuing professional development (CPD) training and Jellicoe lecture at The Eden project near St Austell, Cornwall.
Before joining the LI Mulligan was executive director of the United Nations Association UK and spent four years as chief executive of Environmental Protection UK, formerly the Clean Air Society.
He is a keen environmentalist and spent six months as crew on Greenpeace’s boat, the Rainbow Warrior in the 1990s. He stood for the Hove consituency as a Green Party candidate in the 1997 General Elections achieving 644 votes or 1.3 per cent of the vote share. The seat was won by Ivor Caplin, part of the New Labour landslide.
Mulligan said: "Its an honour and it's great to get on board. It's a really exciting time for the institute. On Tuesday we are launching the Public Health and Landscape - creating healthy places position statement, which is an amazing piece of work.
"That's saying there's a real value to landscape beyond the normal understanding. We as an institute and as a profession pull different ideas and people together to make landscapes that work with people and are sustainable."
The Royal Docks ideas competition launched last week was another reason to be cheerful, Mulligan said."We are not just talking to landscape architects about landscape architecture."
LI president, Sue Illman said: "We are delighted to have selected Phil as our new chief executive. His combination of leadership experience and environmental knowledge perfectly matches our needs for moving the Landscape Institute forward.
"In the run up to the 2015 election, Phil’s interests and experience will be a major asset in our work with all of the political parties."