In 1967-68, O'Neill was a student at the United States Army Ordnance Center and School at Aberdeen Proving Ground.

He then spent 1971-72 at the United States Army Command and General Staff College, and then returned to Rice University, completing his Ph.D. in Physics in August 1974.

He then spent the second half of 1983 as Chief of Staff of the United States Army Missile Command at Redstone Arsenal.

In 1996, O'Neill joined Lockheed Martin as Vice President for Operations and Best Practices in the Space and Strategic Missiles Division.

He left Lockheed Martin in 2006, becoming Chairman of the United States National Academies's Board on Army Science and Technology.