Shaffer was born in rural York, Pennsylvania, which lies approximately twenty miles from the AT, and which he always made his home. In the late 1930s he hiked with a neighbor and close friend, Walter Winemiller, and they made plans to hike the whole of the AT together, after the war that they anticipated the US would eventually enter.
Shaffer enlisted in the army in 1941, was well along in his training at the time of the Pearl Harbor attack, and did arduous and risky service as a forward-area radioman in the South Pacific into 1945. His friend Winemiller served in the Pacific Theater as well, and died in the Iwo Jima landings. Shaffer said he did the trail to "walk the war out of my system".
In 1948, he began the journey from Mt. Oglethorpe, in Georgia (the trail's southern end at that time). With sparse equipment that would be regarded as grossly inadequate by most of the through-hikers since – he used worn boots, his army rucksack, and no stove or tent – he reached Mt. Katahdin in Maine, in 124 days, averaging 17 miles per day. Especially after he overcame the skepticism of Appalachian Trail Conference officials (who initially believed his claim of completing the route was obviously fraudulent), his trip raised public awareness of the Trail. He privately published his memoir of the experience; his book, Walking With Spring (ISBN 0-917953-84-3), reflects the experience of most AT hikers, that the project of making the whole trip in the northward direction (the most common choice), is furthered by a start timed to the weather in the Georgia mountains, and by continually taking advantage of the northward progress of milder weather.
In 1965 Shaffer hiked in 99 days from Maine to Springer Mountain, which had recently replaced Oglethorpe as the Trail's Georgia end, becoming the first person to complete a trip in each direction.
In 1982, the Appalachian Trail Conference published Shaffer's Walking With Spring commercially; it is now called "a classic trail diary".
In 1998, he made another northward through-hike (at age 79) from May 2 to October 21 (six days past official closing of the state park), in 174 days, for the 50th anniversary of his first one, with David Donaldson (known as "The Spirit of '48"). He later developed his notes from this trip, under the working title "Ode to the Appalachian Trail", into The Appalachian Trail: Calling Me Back To The Hills.
Shaffer was diagnosed with liver cancer, and died of its complications soon after on May 5, 2002. Donaldson, his most recent through-hike companion, was at his bedside.
On June 17, 2011, he was inducted into the Appalachian Trail Hall of Fame at the Appalachian Trail Museum as a charter member.