The Sequoyah State Park Trail System consists of four hiking trails and interpretive trail suited for beginner to intermediate-level hikers. Located in the Paradise Cove area, Eagles Roost Interpretive Trail is a 1.25 mile long loop that takes guests through a wooded area dotted with oak and hickory trees and along the Fort Gibson Lake flood plains. This beautiful area is a popular roosting area for bald eagles during the winter months.

The interpretive trail within Sequoyah State Park is called the Fossil Trail. This 1/4 mile trail, located south of the nature center, showcases fossils formed between 280 million and 345 million years ago including crinoid stems from marine animals, bivalvia molluscs and shark teeth.

Two of the hiking trails begin near the Sequoyah Lodge. The first, the Three Forks Trail, consists of two loops. One loop is 1/2 mile long and the other is 1.5 miles long, which runs from the Choctaw Campground to the lodge area. The Sequoyah Fitness Trail is 3/4 mile long. It begins at the lodge and winds along the shore of Fort Gibson Lake. In addition to special areas designed for exercise, the trail also has markers describing the cultural and natural history of the park.

At 14+ miles long, the Whispering Pines Mountain Bike Trail is by far the longest trail in the park. Open to beginner to intermediate-level mountain bikers and hikers, this trail offers many entry points. Roughly three quarters of the trail is off road, while the rest is paved.