On Thursday, the Maryland medical examiner ruled Flanagan's death a suicide.
Flanagan was 59. He is survived by his wife, Alex, and daughters Kerry, Kathryn and Kendall.
Flanagan's family released a statement on Thursday that read:
"We thank you for your support and kind words at this difficult time. Thank you for respecting our privacy as we grieve.
"A private memorial will be held at a later date."
"I am so sorry to hear about Mike's passing," Hall of Famer Cal Ripken said in a statement to Mid-Atlantic Sports Network. "He was a good friend and teammate and our thoughts are with Alex and his family. Mike was an Oriole through and through and he'll be sorely missed by family, friends and fans. This is a sad day."
The emergency call notified authorities of a death in the 15000 block of York Road in Sparks, Md., according to police spokeswoman Elise Armacost. Initial reports revealed that the body was discovered on a trail on the grounds. Sparks is located about 18 miles north of the site of the Orioles' former ballpark, Memorial Stadium.
"It is with deep sadness that I learned of the death of my friend Mike Flanagan," Orioles managing partner Peter Angelos said in a statement. "In over a quarter century with the organization, Flanny became an integral part of the Orioles family, for his accomplishments both on and off the field.
"His loss will be felt deeply and profoundly by all of us with the ballclub and by Orioles fans everywhere who admired him. On behalf of the club, I extend my condolences to his wife Alex and daughters Kerry, Kathryn and Kendall."
Flanagan, selected in the seventh round of the 1973 Draft, spent 18 years in the Majors -- 15 with the Orioles, with whom he compiled a 141-116 record, a 3.89 ERA and 1,297 strikeouts. Flanagan earned the 1979 American League Cy Young Award after posting a 23-9 record, 3.09 ERA and 190 strikeouts, leading Baltimore to the AL pennant before falling to the Pittsburgh Pirates in the World Series in seven games. The left-hander went 1-1 in 15 innings with 13 strikeouts in the Fall Classic.
"He was fantastic that year," said former O's teammate and current YES broadcaster Ken Singleton, who played with Flanagan from 1975-84 and hit 35 home runs in '79. "The first time I ever met Mike's dad, he thanked me for hitting all the home runs  in the games his son pitched. It just so happened I think I was hitting one every fourth or fifth day, and he was on the mound."
Flanagan later returned to the World Series in 1983, making one start as the Orioles eventually took the Series, 4-1, and provided him with his lone ring. Flanagan went 12-4 with a 3.30 ERA in 20 starts that season.
"He was a good pitcher, an even better teammate," said Singleton, whose home is close to Flanagan's in Sparks. "His locker was only a couple down from mine at Memorial Stadium. I played with him for 10 years. He's a good man. He's one of the best pitchers the Orioles ever had."
Flanagan spent three-plus seasons with the Blue Jays from 1987-90 before returning to Baltimore in '91 and spending the final two seasons of his career as a reliever. In '91, Flanagan was part of a four-pitcher no-hitter, which stands as the last no-hitter thrown by the franchise.
Flanagan retired following the 1992 season with a career record of 167-143 and 3.90 ERA. He struck out 1,491 batters in 526 games.
"He was one of our family," said Hall of Fame right-hander Jim Palmer, a former teammate of Flanagan's and his fellow color commentator on Orioles telecasts. "Great friend, great competitor.
"He was like a breath of fresh air with his humor and insight and all those things. He was just a terrific guy."
Current A's manager Bob Melvin, another former teammate, said he was shocked to hear of the news of Flanagan's death.
"I think the world of him," Melvin said. "I was teammates with him just the one year in Baltimore, but we've had a friendship since. He struck Travis Fryman out to end Memorial Stadium's history, and I was catching, and he had a photo of it blown up years later, framed, and gave it to me.
"He was a man's man, and the ultimate baseball guy's guy. He was a leader, just someone you really looked up to and respected. ... That's just unbelievable, completely shocking."
Following his retirement, Flanagan was a common presence around the Orioles' organization, serving as a broadcaster from 1996-97 and 1999-2002 before moving into the front office on Dec. 4, 2002, when he took the position of vice president for baseball operations, working alongside vice president Jim Beattie, giving Baltimore de facto dual general managers. In 2005, Flanagan was named executive vice president for baseball operations, a position he held until 2008.
Flanagan, whose grandfather Ed Sr. and father Ed Jr. both played in the Red Sox organization, was voted into the Orioles Hall of Fame in 1994.
During his time in the Orioles' front office, Flanagan claimed right-hander Jeremy Guthrie off waivers from the Indians in 2007. They shared a special bond -- and a uniform number -- since then, which shows the impact Flanagan had on the Baltimore organization.
"Since the day I was given No. 46, I've had thousands of people tell me that was the number of their favorite pitcher for the Orioles when they were growing up," Guthrie said. "So from Day 1, I think I've been reminded of the legacy and of the work that Mike did not only as a player, but also as a member of the community in Baltimore.
"It's always been special and now I think it takes on even a new level. He's not going to be forgotten soon, that's for sure."