Yes. In fact a large band fought in the Trans-Mississippi for the South organized as cavalry under Chief Stand Watie he led a mixed bag of Seminole and Cherokee. He was the last officer of flag rank (general) to surrender from the Confederacy.

Though many plains Indians did remain loyal. A notable one was Gen. Ely Parker who served as Grant's Adjutant and was a full blooded Seneca. He was the one who actually wrote the terms and instrument of surrender signed by Lee.

Also in 1862 the Sioux began an uprising from the reservations in the Dakotas though it was largely unconnected with the larger war.

While additional answers are also appreciated, you'll probably also want to check out The Civil War and Native Americans section of our FAQs. I don't think that category has been updated since I made this post though, and that's been over a year ago. I know this question has come up a few other times since then so I might need to check if any of the more recent posts should be added to the FAQs.