Marlins president David Samson last week pledged to exclude Boras after the agent complained about the Marlins' handling of another Boras client, outfielder Marcell Ozuna, who is believed to be on the trading block.
Fernandez's innings will be closely watched in 2016, as they were this year after he returned in July from Tommy John surgery. He said his surgeon and the team doctor also will be involved in discussions regarding how he's used, as they have been in the past.
"I do not know what all this is all about, but Scott Boras will be there, because he's my agent," Fernandez said Friday. "I get to decide who is going to be on my phone calls. It's that simple."
Fernandez made his comments at a team community event at Marlins Park, where he handed out Thanksgiving turkeys.
The feud between the team and Boras reduces the already-slim chance the Marlins will sign Fernandez to a long-term contract. The spat has also stirred speculation the Marlins might trade Fernandez this offseason, but he said he expects to pitch for Miami in 2016.
"I'm looking forward to being with my teammates and winning some ballgames, get ready to go to spring training healthy and have a nice long year with the boys," he said. "Hopefully we get the opportunity to win the World Series. That's the main goal."
Fernandez, who made $651,000 in 2015, is arbitration-eligible for the first time this offseason. The right-hander rejected a multiyear offer before the 2015 season, Samson has said, and can become a free agent after the 2018 season.
The Associated Press contributed to this report.