Many of them were dressed in purple, BTS' signature colour, and carried large banners and photographs of the two K-pop idols.
South Korea requires all able-bodied men aged 18 to 28 to serve for about two years in the military so the country can be ready to fight the North.
On Tuesday, Hybe displayed a banner saying "We are back", along with the official logos of BTS and ARMY - an acronym for the band's fan group, which stands for Adorable Representative MC for Youth - on its building.
"This feels incredible. To be here in Seoul, to see the place where BTS grew up and started singing and dancing. It's amazing," Janya, who flew in from the UK, told The Korea Herald.
"I want to say to RM and V that you are a massive inspiration, and I love you so much!" the 28-year-old said.
"It's been a long, long time without you. I'm so glad you're back and finally free to do whatever you want to do," said Ivory from Australia.
Hannah Chung, who lives in London, told AFP news agency that she planned her trip two years ago "because I knew the members will be out by then".
She is counting on a chance to see the band at the annual BTS Festa, a celebration of the band's debut, that will take place on Friday.
Earlier during their discharge in Chuncheon, RM thanked fans for waiting for them to complete their national duties.
"Now, I'm ready to hit the ground running again as RM of BTS. Thank you to everyone who waited and looked after us," he said.
V said the military tenure was a "time for me to reset both physically and mentally".
"I really want to run to ARMY as soon as I can. Thank you for waiting for us during our military service," he said.