Ter Stegen, 33, made just nine appearances last season after injuring his knee and missed the start of the current campaign after undergoing surgery on a back problem.
The German international returned to fitness earlier this month but has found himself on the bench in the last two games behind García, a €25 million ($29m) summer signing from Espanyol.
"This is his decision," Flick said in a news conference Friday when asked if Ter Stegen could leave in January in order to fight for a place in Germany's World Cup squad next summer.
"We spoke about his situation and I respect Marc a lot because he's a fantastic goalkeeper. He's a really good player for us, also a good human for the team, but at the end it's his decision and he has to decide, so it's about that."
Ter Stegen has made 422 appearances since signing from Borussia Mönchengladbach in 2014, winning 17 trophies in that time, but that counts for little now.
He is not even guaranteed to get minutes in Tuesday's Copa del Rey tie away at fourth-tier side Guadalajara.
García will not be involved as he is given time off ahead of Sunday's LaLiga trip to Villarreal, but Flick says he has not decided whether that will mean game time for Ter Stegen or Wojciech Szczesny.
"Joan will rest," Flick said. "But today is not the day to make the decisions [on who will play]. I want to wait until tomorrow.
"Of course, Marc is a fantastic goalkeeper. In the goal, we have three excellent players. I am really happy about this. We will see what happens.
"But it's clear what I said before: Joan is No.1. From there, we will see what happens. Tek [Szczęsny] played last season a fantastic season, we won with him three titles. Also, this season, when Joan was injured, he gave us stability.
"For me, Tek is not only on the pitch, but also in the dressing room, a really important player for us."
Holders Barça enter the Copa in the round of 32 against Guadalajara, who beat second-division side AD Ceuta to make it this far.
Flick says his players are ready for the challenge of facing a lower league team as they look to take their good league form -- winning seven games in a row to open up a seven-point lead over Real Madrid at the top -- into the cup.
"It's about the attitude and the mentality we show," the German coach added. "The players know it. It's about how we start the game, this is the basics of this match.
"In these matches you have to win. We play in LaLiga and we are the favourites, so this is what I want to see from the team. They have to be ready and show our quality on the pitch."
