Gilligan is the club`s longest-serving player having signed in 2005 and has made more than 200 appearances for the club, but he has now joined the Gulls until at least March 9.
He has recently lost his place after the Cobblers signed Josh Walker and Francis Laurent in the January transfer window.
Manager Ian Sampson said: "This is a good opportunity for Ryan to go out and play some games.
"We have strengthened the squad in the last few weeks and competition for places, particularly in midfield, is tough.
"Ryan has seen his chances restricted in the last few weeks and with Liam Davis, Kevin Thornton and Andy Holt coming back to fitness it made sense to let Ryan move out on loan. He is keen to go and play some football and I am sure he will do a good job for them."
Source: PA
Source: PA