The former Premier League champions dropped down into the third tier of English football for the first time since 1980 on Sunday, despite their final-day victory over Brentford.
"Paul Senior has today resigned from his role as director of football and operations," said a statement on Blackburn's official website. "The club would like to thank Paul for his efforts and wish him well in his future endeavours.
"Paul would like to go on record by wishing Tony Mowbray, the club's loyal and hard-working staff and fantastic fans the very best good fortune forward."
Senior, who current manager Mowbray claimed was the only member of the hierarchy he spoke to prior to taking the job in February, had been hired just 123 days ago with part of his remit to oversee recruitment.