O'Brien, currently a presidential envoy for hostage affairs at the U.S. Department of State, has a long history in Republican foreign policy circles.
"I have worked long & hard with Robert. He will do a great job!" Trump wrote on Twitter.
He had served under the George W. Bush and Barack Obama administrations.
Mr O'Brien served as a major in the U.S. Army Reserve. Former President Bush appointed him in 2005 to serve as a representative to the U.N. general assembly.
He is an attorney from Los Angeles who has served as a foreign policy adviser to several Republican presidential campaigns, handled a number of high profile legal cases and previously served in several State Department positions, including as an alternative representative to the U.N. General Assembly in 2005.
Trump had been weighing a number of potential replacements after Bolton left the post last week following disagreements with the president over his handling of North Korea and Venezuela.
His previous national security advisers were H.R. McMaster, who was replaced by Bolton in March 2018, and Michael Flynn, who was fired shortly after taking the role and later pleaded guilty to lying to the FBI.