The Scottish comic, 44, has sparked anger in the past with a string of jokes, causing outrage by targeting Rebecca Adlington's appearance as well as Katie Price and her disabled son Harvey.
His quip about Olympic swimming champion Adlington earned a reprimand from the BBC Trust, which branded it "humiliating".
Boyle's remark was made on satirical series Mock The Week on BBC2, and he will be back on the channel with a show that could make "challenging viewing".
But new BBC2 controller Patrick Holland said the channel had to feel more contemporary.
"If we're going to be making the channel feel more more contemporary and more relevant, we want to be looking at the issues of the day and Frankie is one of those voices that does that," he said.
"He's an extraordinarily strong voice and a very passionate voice. He has the ability to explore some of the issues of the day.
"I think it will be challenging viewing but it's important that voices like Frankie's are heard on BBC2."
Speaking after unveiling a series of programmes to air over the spring/summer, he added: "I said when I first got the job at the channel that voices like Frankie's were really important."
Mr Holland said he was "keen that Frankie comes back".
"Frankie knows that he's going to be working on the BBC and ...there are BBC guidelines and the audience expects those guidelines.
"Frankie's really keen to be back on BBC2.
"It's important that comedy is responding to what's happening in the world," he said.
Boyle has previously described the BBC as a ''great institution'' which had become ''cravenly afraid of giving offence''.
In 2011, the star was censured by media watchdog Ofcom for "offensive" remarks made about Price and her son Harvey, on Channel 4.
His routine appeared to target and mock the mental and physical disabilities of the eight year-old, Ofcom said.
American Autopsy - Boyle's take on US politics - aired on the BBC iPlayer followed by BBC2 last year, with guest comics and experts.
But the new programme - with details being kept under wraps - is expected to feature several episodes and will take the format of a topical news show.