A spokesman for SAC Capital said the allegations have "no merit" and Cohen "will fight this charge vigorously."
"Steve Cohen acted appropriately at all times," spokesman Jonathan Gasthalter said in a statement.
The SEC's action against SAC, one of the best-known hedge funds, stemmed from the wide-ranging government investigation of insider trading at U.S. hedge funds. Earlier this year, an affiliate of SAC Capital agreed to pay $615 million to resolve the SEC's insider trading charges against the firm. The agency said it was the largest insider trading settlement ever.
Cohen is one of the highest profile figures in American finance and one of the world's richest men. He is among the handful of upper-tier hedge fund managers who pull in about $1 billion a year in compensation.
His hedge fund until recently managed portfolios of more than $15 billion in assets, according to the SEC.