NBA Commissioner Adam Silver says he expects players to stand for the national anthem, which is a league rule unlike the protocols in American football.
Mr Silver added he wanted basketballers to remain active in their communities and take part in what can be difficult discussions about racism and freedom of speech.
But he says NBA players understand it is important to show respect for the flag.
Mr Silver did not say what repercussions there might be if any players refused to stand.
"If that were to happen, we'll deal with it when it happens," he said.
Mr Silver spoke following the NBA's board of governors meetings on Thursday, during which owners passed rules designed to prevent healthy players from sitting out games, and teams from losing games on purpose - "tanking" - to improve their draft position.
But the NBA has protocols for the playing of 'The Star-Spangled Banner'.
NBA player LeBron James has been most vocal about the stoush between the NFL and US President Donald Trump.
After Mr Trump uninvited Golden State Warriors player Stephen Curry to the White House, the Cleveland Cavaliers star called the president a 'bum'.
This was followed by NFL team members, coaches and owners taking the knee and linking arms to protest for black civil rights after the president slammed players for engaging in the act.
Mr Trump, who last week called for the NFL to sack players taking a knee in protest at the treatment of African-Americans by police, tweeted on Tuesday that football needed to update its rules.
"The NFL has all sorts of rules and regulations. The only way out for them is to set a rule that you can't kneel during our National Anthem!", Trump wrote.
The NBA begins pre-season games this weekend. The regular season starts October 17.
