The 20-year-old is on loan at the League Two leaders from MK Dons until the end of January.
Flanagan told BBC Radio Kent: "I like a big run of games. Consistency is a really big thing when you're a defender.
"I've moved down and am nice and close. I'm enjoying the place and fully committed to it.
"When it comes to January we'll sit down with everybody we need to sit down with. We'll find out what happens but it will be down to the two clubs at the end of the day."
Gillingham are playing Burton Albion this afternoon.