The comments come weeks after French President Emmanuel Macron called for the creation of a "true, European army" in a bid to ensure that Europe would not "become a plaything of great powers".
Mr Williamson, speaking at Defence questions in the Commons, said:
"Let's make it absolutely clear: Britain is not going to be participating in a European army.
"The cornerstone of our defence in the United Kingdom on continental Europe and the North Atlantic is the North Atlantic Treaty Organisation and not the European Union."
Later in the question session, Tory MP Dr Julian Lewis, in a nod to the Brexit negotiations, referenced the success of the 1987 Intermediate-Range Nuclear Forces Treaty between the United States and Soviet Union and asked Mr Williamson if the UK could learn any lessons from it.
Dr Lewis, who chairs the Commons Defence Committee, said: "The Intermediate-Range Nuclear Forces Treaty of 1987 was based on the zero option offer, which was a great two-sided deal between the Soviet Union and the West.
"Does the Secretary of State think there are any lessons to be drawn from the negotiations that led to that successful deal - in that the West faced down the Soviet Union, walked out or at least allowed the Soviet Union to walk out without a deal when the Russians refused to accept the zero option offer, and waited for them to come back and do a genuine deal that benefited both sides.
"Does he think the lesson of that successful two-sided deal has any lessons to teach us for certain other negations that have worked out so far a lot less happily?"
Mr Williamson responded: "I can't imagine what he's referring to."
Tory MP Marcus Fysh said the Withdrawal Agreement would commit the UK to "all of the state aid prevention rules" of the EU, adding: "It wouldn't give the UK the exemption for the defence industry to those state aid rules.
"On what planet could we possibly support such a measure that would destroy jobs across this nation and make our defence industry uncompetitive?"
Mr Williamson replied: "What we're looking at is making sure we keep the freedom and independence that we need to have in terms of defence procurement, and that's integral to everything we're going to do going forward.
"What we'll want to do is to see if there are other options in terms of having some access to some programmes within the European Union, and, if that works for Britain, we'll consider that."
Shadow defence minister Wayne David said the cost of developing a British alternative to the Galileo satellite navigation project could be between £3 billion and £5 billion, and asked if the Treasury has agreed to pay this sum.
Mr Williamson, in his reply, praised British expertise on satellite technology and said: "We're more than capable of delivering that system with international allies.
"There are more international allies around the globe than purely the European Union - whether it's the United States, Japan, Australia, South Korea, and many others that we can work with."