Allen, who has been criticized for how he has handled contract negotiations between the guild and the Alliance of Motion Picture and Television Producers in recent months, told SAG staff via email that he was leaving, Variety.com said.
SAG and AMPTP's last contract expired June 30. The two entities have not been able to hammer out a new pact since, with a faction inside the SAG membership blaming Allen for the stalemate.
Former SAG general counsel David White is expected to take over as interim executive director, the entertainment industry trade newspaper said.
Allen reportedly stepped down from his position shortly after a "written assent" document -- signed by 53 percent of the national board and authorizing the replacement of Allen as national executive director -- was delievered to SAG's Hollywood headquarters.
"This is the darkest day within my memory. It kills democracy at SAG," SAG President Alan Rosenberg told Variety.com.