Seau, a 1990s star with the San Diego Chargers, died of a self-inflicted gunshot wound on Wednesday, after his girlfriend found him unconscious.
His death followed the 2011 suicide of former Chicago Bears star Dave Duerson.
Their deaths have led to questions over the effect of concussions on the brains of professional football players.
"They [the family] believe that through allowing this procedure, it will allow the betterment of other individuals and athletes in the years ahead," Pastor Shawn Mitchell, former chaplain for the Chargers, told the Reuters news agency.
"Their thought is, if it can benefit others, then it's probably worth going forward with."
The San Diego County Medical Examiner's Office said Seau's brain would need to be conducted by outside researchers.
Seau's family has not said whether they believe concussions could have played a role in the football star's death.
But recent studies have found a connection between repeated concussions and chronic traumatic encephalopathy, a disease with symptoms including memory loss and mood swings.
On Thursday, a more than a hundred former National Football League players filed a lawsuit claiming the National Football League (NFL) deliberately hid the dangers of concussions from them.
They join an additional 1,500 former NFL players who have put their names to similar lawsuits.
Duerson's family have already filed a wrongful death lawsuit against the NFL, alleging that the organisation did not do enough to prevent or treat concussions that had damaged his brain. He died in February 2011.
Seau's ex-wife, Gina, told the Associated Press news agency that over the course of his 20-year football career, Seau also suffered concussions.
But his relatives and friends say they did not know of any issues that may have led to his death. Police have said they did not find a suicide note.
In 2010, Seau drove his car off a cliff hours after he had been arrested on suspicion of domestic violence.
Seau starred with his hometown San Diego Chargers for 13 years before playing with the Miami Dolphins and New England Patriots.
He was inducted into the Chargers Hall of Fame in 2010.
The family of former American football star Junior Seau has donated his brain for research into the effects of head trauma on football players.