Eccles, who was a member of BSkyB's 12-member executive management committee, is set to depart before the end of the year.
He is not thought to have accepted a new position, nor is his departure believed to be connected with BSkyB's effectiveness review, announced earlier this year (PRWeek, 3 June).
In an internal email to staff, CEO James Murdoch described Eccles's decision to quit as 'personal'.
He added that Eccles had been 'instrumental in transforming the reputation of BSkyB into a modern, respected FTSE entertainment company'.
The broadcaster has lined up Eccles's successor and is set to make an announcement within weeks.
Eccles, a former adviser to ex-culture secretary Chris Smith, joined BSkyB in 2000 and saw his brief expanded to cover corporate affairs, internal comms and programme publicity.
He was previously corporate comms director at British Interactive Broadcasting, a consortium set up by BSkyB, BT, Matsushita Electric and HSBC Holdings to deliver digital and interactive services under the Open name.
Eccles joined BIB in 1998 from the Department for Culture, Media and Sport, where he was special adviser to Smith.
He oversees 65 staff at BSkyB covering corporate responsibility and comms, consumer PR, programme publicity and information, and internal comms.