"I have the highest regard for David Montgomery, as does everyone in our industry," Gillick said in a statement. "I am glad to be of assistance to the Phillies."
Montgomery will return to work when he is fully recovered, according to the team.
Gillick, who turned 77 last week, joined the organization following the 2005 season when he was hired to replace Ed Wade as general manager. During Gillick's 3-year tenure as GM, the Phillies won the 2008 World Series and the first two of five straight National League East titles.
Gillick, who also won two World Series rings as the GM of the Toronto Blue Jays in 1992 and 1993, was inducted into the National Baseball Hall of Fame in 2011.
Gillick stepped down as Phillies GM following the 2008 World Series, when his contract expired. One of his top lieutenants, Ruben Amaro Jr., was named as his replacement.
Amaro helped guide the Phillies to another National League pennant and three more division championships. But Amaro has been under heavy scrutiny in the last 2 years, when the team has had a losing record despite having one of the top three Opening Day payrolls in baseball.
Although he stepped down as GM, Gillick stayed on with the organization for the 2009 season as a senior adviser to Montgomery and Amaro, a role he has held for each of the last six seasons. He has remained one of Amaro's top confidants during that time.
Montgomery, 68, has been with the Phillies since 1971, working his way up through the organizational ranks before succeeding Bill Giles as general partner, president and chief executive officer of the team in 1997. A man respected not only within the organization but throughout all of baseball, too, Montgomery is in his 44th season with the Phillies.
Montgomery's May surgery involved having a bone removed from his leg and transplanted into his mouth. He was expected to make a full recovery from cancer.
"It's sad; it's tough," first baseman Ryan Howard at the time. "Our thoughts and prayers go to him and his family."
"In a lot of ways, [he's] our biggest fan," manager Ryne Sandberg said in May. "From my experience here the last 4 years, he's the guy who sets the tone, as far as it being a family oriented organization - first-class, the right way.
"He's the leader of the organization. He set the tone at the top, no matter if it's the players reaching out in the community for their events . . . or the way the players have it so good, as far as being treated first-class. It all starts with David Montgomery."
On Twitter: @ryanlawrence21