O'Donovan joined the Cobblers from Coventry City in January, and after scoring six goals in 16 appearances, Boothroyd believes that the 27-year-old can help the club to promotion next season.
The former Watford boss told the Northampton's official website: "There was considerable interest in Roy from a number of clubs from a higher level and we had to work hard to secure Roy's signature.
"But Roy feels settled with us and we are delighted that we have been able to keep him. I thought he was terrific for us towards the end of the season and once he has got a full pre-season under his belt, I think we will have a real player there."
Northampton missed out on promotion to League One last season after losing to Bradford City in the playoff final.