Muhammad Ali Jr was detained and questioned at a Washington airport before being allowed to board a flight to Fort Lauderdale, his lawyer said.
The incident came after a meeting with politicians to discuss a separate airport detention last month.
Mr Ali and his mother, Khalilah Camacho Ali, were stopped at the Fort Lauderdale-Hollywood International Airport after returning from Jamaica on February 7.
They travelled to Washington on Wednesday without incident to speak to members of a congressional subcommittee on border security about that experience.
But attorney Chris Mancini said that when Mr Ali attempted to board a JetBlue Airways flight home to Florida that day he was detained for 20 minutes.
Mr Mancini said Mr Ali spoke to Department of Homeland Security (DHS) officials by telephone and showed his driver's licence and passport before he was allowed to board.
"None of this was happening Wednesday," Mr Mancini said in a telephone interview on Friday afternoon as he was travelling with the Alis. "Going to Washington obviously opened up a can of worms at DHS."
Florida Democratic Congresswoman Debbie Wasserman Schultz, who was on the same flight, tweeted a photo with Mr Ali after he was allowed to board and wrote: "On way home on DOMESTIC FLIGHT Muhammad Ali Jr. detained AGAIN ... Religiously profiling son of 'The Greatest' will not make us safe."
The mother and son, both born in the United States, have said in interviews that they believe they have been stopped because they are Muslim with Arabic names.
Earlier this week, they announced a campaign for religious freedom in the spirit of the boxing icon, supported by ex-boxing greats Evander Holyfield, Larry Holmes, Roberto Duran among others.
They say they are opposed to President Donald Trump's travel ban, which they feel unfairly targets Muslims.
A spokeswoman for JetBlue referred questions to DHS officials.