Brannagan was on the verge of completing a move a fortnight ago, although he featured in the Reds' final pre-season friendly against Mainz in Germany just days after it was reported a deal had been agreed.
But the 20-year-old's move fell through after Wigan's reluctance to agree to a stipulation which required him to play in 75 per-cent of the club's fixtures when fully fit.
Wigan had earlier been hesitant to agree to the clause, but changed their minds soon after Brannagan had played against them in a friendly in Greater Manchester at the end of July.
But they reversed their decision once more, which led to the deal falling apart.
The Latics' failure to play Brannagan in a specific number of matches would have seen them hit with a six-figure fine, with Liverpool keen to ensure Brannagan plays regularly if he is to go out on loan.
The Academy graduate had previously indicated a willingness to have a spell in the lower leagues in order to "experience men's football" and could yet seal a move elsewhere.
But any move is dependent on a club agreeing to Liverpool's demands as they look to secure the best moves for their promising youngsters.
Brannagan staying put at Liverpool for the timebeing
But he won't be joining Liverpool teammate Adam Bogdan at the DW Stadium after Wigan - managed by Gary Caldwell - had seconds thoughts on their deal for Brannagan.
Earlier in the summer, they had been keen to pay as much as £1 million to secure a permanent deal for the Manchester-born midfielder, but Liverpool view Brannagan as one of their brightest prospects.
The No.25, who has been at Anfield since the age of five, made nine first-team appearances in a breakthrough campaign last season - six of those coming under Jürgen Klopp, including his first run-out in the Premier League.
He featured regularly over the course of the club's recent pre-season too and, should he remain on Merseyside until the end of the current transfer window, could emerge as a useful back-up option in central midfield.
Brannagan could also feature regularly for Michael Beale's Under-23s side in their Premier League 2 campaign, having been the captain of the Under-21s at times last term.
But he could also join the eight other Reds who have gone out on loan already, with a loan move somewhere else still a possibility - although he remains an important part of Klopp's long-term plans at Liverpool.