Raphinha, 29, scored 34 goals and provided 26 assists in all competitions last season as Barça won LaLiga, the Copa del Rey and the Spanish Supercopa at the same time as reaching a first Champions League semifinal since 2019.
However, the former Leeds United forward was snubbed when FIFA's Best XI for the year was revealed last Tuesday, with teammate Lamine Yamal, Ousmane Dembélé, Cole Palmer and Jude Bellingham among those included ahead of him.
"I am not happy that you are not asking me, because there is one situation [I want to talk about]," Flick said, unprompted, at the end of his news conference ahead of Sunday's trip to Villarreal in LaLiga.
"It's not a big thing because in general I don't care about these things, but this FIFA Best XI players is a joke, really a joke. When I see there is no Raphinha in the side, it's unbelievable."
The team is voted for by national team head coaches, captains, journalists and fans. Gianluigi Donnarumma, Achraf Hakimi, Willian Pacho, Virgil van Dijk, Nuno Mendes, Vitinha and Pedri completed the lineup.
Raphinha received a total of 12 points in the vote, which was also fewer than Erling Haaland and Kylian Mbappé, two other high profile omissions from the team.
"Raphinha was the player in this team with the greatest influence," Flick continued. "In the Champions League, he had 22 goal contributions, the best in the Champions League.
"When you see the matches he played, how many goals he scored, the assists he had, it's unbelievable. This is really not fair to him. For me, it's a joke. I can't believe it because after the season he had, he deserved it. It's unbelievable."
Raphinha has missed nine games this season due to injury but returned at the end of November and has scored three goals in his last four starts.
He will lead Barça's attack at third-place Villarreal on Sunday, but Flick has lost midfielder Pedri, who won't be risked due to a hamstring problem.
"Pedri's not available," Flick confirmed. "I am not happy about this, but it's part of football. He's injured, but I think for the next game [against Espanyol] he's ready.
"He had a problem with the hamstrings and we take care. The risk is too high. Maybe he could play, but it's too high and if something happens he's out for two months and this is not good."
Barça's trip to Villarreal is their final game of 2025 before LaLiga breaks until January.
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It pits LaLiga leaders Barça, who have won seven league games in a row, against a Villarreal side who are in similarly impressive form having won their last six league games, which has seen them climb to third in the table, four points behind second place Real Madrid but with two games in hand.
The last four meetings between Barça and Villarreal in LaLiga have featured 26 goals, with each team winning two games each.
"Every game is the most important game, every game is difficult," Flick added. "We are playing against an important team, a lot of quality, direct play, I love to see how they play football.
"Congrats to the coach [Marcelino García Toral]. It's an amazing team. They improve a lot the last years, they did it really good."
