As a young man, Tom Brown, Junior, loves to be out in the woods. He especially loves finding clues to what is going on with the wildlife in the woods. He is blessed with the perfect opportunity to learn everything he wants when he makes a best friend in grade school, a boy named Rick who has a wonderful grandfather called Stalking Wolf, an Apache Indian. Rick and Tom both call Stalking Wolf "Grandfather," and the elder has a wonderful way of teaching the boys how to understand the woods, and how to survive and even thrive in conditions that many would call hostile.

The story takes place in the Pine Barrens, a wild and desolate area in New Jersey. As Brown points out, most people consider the Pine Barrens to be dangerous and frightening territory, mainly because it is so unpredictable and wild. However, with Grandfather's training, Tom and Rick learn to navigate the Pine Barrens as easily as many people move around in their own homes. Even when threatened with severe weather, packs of wild dogs, or hunger and thirst, the boys learn to use excellent wilderness skills to master the challenges of the Pine Barrens. To Tom Brown, it is the ideal way of growing up. He admits that if his parents were to know how far he travels during these years, and through what risks, they will have been horrified.

Stalking Wolf teaches the boys how to walk invisibly and silently in the woods, how to build warm, cozy shelters in the worst of weather, how to capture, dress and prepare game, and how never to get lost. This book reveals so many of Grandfather's lessons through Tom Brown's eyes and experiences. Some of the stories are almost impossible to believe, as when Tom hunts and kills a deer with only a knife, tracking and sneaking up on the animal undetected. Finally, when as a young man Rick leaves, Tom spends a whole summer by himself in the woods, just like Thoreau.

After this summer, Tom realizes that he has transformed into a man with powerful tracking skills. He undertakes the great challenge set forth early in the book, where Grandfather describes sneaking up on a bear, smacking it in the tail, and escaping unhurt. Tom survives attacks from wild dogs, evidently a terrible risk in the Barrens, several times in the book. Finally, Tom emerges as a compassionate man who uses his skills to help track people who have been lost or hurt in the Barrens.