The 23-year-old is expected to start against Morecambe in League Two on Saturday, and reach the milestone.
Sampson told BBC Radio Northampton: "When I was 23, I'd only played 10 games. It's a great achievement.
"He's a team player, he's unselfish and he'll play in any position. They're the type of players you need," he added.
"He's well worth his 200 games."
However, Gilligan still has some way to go to better the club record for appearances set by Tommy Fowler, who played 552 matches for the Cobblers between 1946 and 1961.
Manager Sampson himself played 449 times for the club.
Gilligan scored his first goal of the season in the 1-0 win over Stevenage on Saturday, having notched nine last season.
"He'll be disappointed he's not scored more goals this season but he'll be happy to have got off the mark," said Sampson. "He does a good job for the team."
Source: BBC Sport
Source: BBC Sport