Around 150 British personnel were stationed at Constanța on Quick Reaction Alert, providing a "strong deterrent" to Russia according to one RAF officer.
Making the announcement on Wednesday, Mr Williamson said: "The deployment of RAF Typhoons to Romania last year – where our pilots policed Romanian territorial airspace – demonstrated the benefits of our vibrant defence relationship to European security.
"Today’s discussions underlined our two countries’ commitment to deepening that relationship for many years to come."
The MOD said the signed document confirms the two countries will aim to build a new industrials partnership to develop cutting edge defence capabilities.
Direct cooperation on defence intelligence, military medicine and health support services were also mentioned as part of the agreement.