The player will miss key matches against Bayern and Borussia Dortmund among others as Schalke, in fourth place, fight for a Champions League spot.
"As opposed to the DFB control committee, we do not believe that it was unsportsmanlike conduct," Schalke said in a statement.
"This is not part of Klaas-Jan. The red card was justified but a ban of six games is in our view is clearly too high. That is why we lodged an appeal."
Huntelaar said he was surprised by the red card.
"I was completely perplexed with the red card because that challenge did not really look that hard and because I am not a hard player," he said.
"In my entire time in the Bundesliga I have only once been sent off and that with a double booking."
Schalke, who face Real Madrid in the Champions League last 16 this month, are fourth in the Bundesliga and visit leaders Bayern Munich on Tuesday.
Dutch international Huntelaar, 31, who has played in 17 of the 18 league games this season, has netted seven times.
(Reporting by Karolos Grohmann, editing by Tony Jimenez)
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