After relegation from the Scottish Premier League last season, Gretna subsequently went out of business to open up a place in the Third Division.
A total of five clubs applied to take Gretna's spot, with Cove Rangers, Edinburgh City, Preston Athletic and Spartans also in the running.
However, at a meeting at Hampden on Thursday, the 29 SFL clubs voted to accept Annan Athletic in to the league.
With a minimum of 15 votes required to gain entry to the SFL, three rounds of voting were needed before the East of Scotland League side's place was confirmed.
They polled 17 votes in the final round, with Cove Rangers their closest challengers with 12 votes.
Annan chairman Henry McClelland said: "It's just sunk in, but it's been a long time coming.
"We've not been working towards this for only a few months - we've been working for this since we played Stranraer in 1979.
"We have been rewarded for all our work since then."