"Woods Runner" is the story of Samuel Smith, a thirteen-year-old boy living on the western frontier of Pennsylvania in 1776. Samuel lives with his parents, Olin and Abigail, in a settlement of small cabins surrounded by thick woods. Samuel's parents are newcomers to the frontier, having been raised and educated in eastern cities. Samuel, however, has grown up on the frontier and is most at home walking and hunting in the deep forest. His skills have far outpaced those of his parents and he has become the provider for his family.

While on a solitary hunting excursion several miles from home, Samuel sights a plume of smoke rising from his settlement. He rushes back to find that the small group of cabins has been burned to the ground and several settlers brutally killed. Using his tracking skills, he determines that his parents survived the attack and were carried away as captives. Later Samuel learns the attackers were British soldiers assisted by Iroquois Indians and that the attacks were part of the larger Revolutionary War that was now in its early days.

As Samuel follows the trail of his parents' captors, he rescues an eight-year-old girl named Annie Clark whose parents are killed by Hessian mercenaries fighting for the British. Moving through the woods and underbrush to avoid detection, they make their way to New York City where Samuel believes his parents are being held as prisoners of war. On the road to the city, they are helped by a Scottish tinker named Abner McDougal who turns out to be actively engaged in spying against the British.

With Abner's help, Samuel makes his way to British-controlled New York City, locates his parents, and rescues them in a daring escape across the Hudson River to New Jersey. Led by Samuel, the family, which now includes Annie as an adopted daughter, makes its way cross country toward Philadelphia, which is held by colonial forces. Samuel narrowly escapes death when he stumbles onto a British detachment in the woods, but is saved by rebel soldiers who fire on the unit and escort his family to safety. Samuel later returns to the fighting in support of a group of riflemen.

"Woods Runner" also contains brief historical notes which are alternated between the narrative passages and which provide factual information about life in wartime in eighteenth-century America. These sections, the author explains, are to provide as realistic a backdrop as possible for the narrative elements of the story. They serve to accentuate the challenges endured by the main character and depict the sometimes ugly reality faced by children during wartime.