No successor has yet been appointed, with interviews for the position expected to take place in September.
PRWeek understands the parting of ways is mutual and Boughen is expected to take a short break before exploring other opportunities.
"Aileen has long been intending to seek fresh challenges but agreed to stay and oversee a smooth transition to the new Government," Alex Hamilton, deputy head of news at BIS, told PRWeek.
Boughen could not be reached for comment as she is currently on holiday and is scheduled to return to work on 17 August.
Before moving into PR, Boughen started work at the Leicester Mercury as assistant news editor. She held the position of head of comms at the National Communications Union for just under 10 years, before moving on to BT where she worked her way up from senior press officer to director of comms for BT Wholesale.
In 2005, Boughen briefly ran her own agency called Communicator Public Relations before taking up her current role at BIS.