Thayer was Second Vice-President of the Pennsylvania Railroad. He was married to Marian Longstreth Morris and they had two daughters: Margaret "Peggy" and Pauline, and two sons, one of whom, Jack Thayer, accompanied them on their trip to Europe in 1912.
The family were preparing for bed when the collision occurred. Jack went up immediately to investigate, he returned to their stateroom and they followed him back on deck.
As the boats were prepared for lowering John and Jack said good bye to Marian. They believed she got away in a boat but Second-in-command First Class Steward George Charles Dodd advised them that she was still on board. They found her again and, after losing Jack in the crowd, John saw Marian safely into Lifeboat 4.
Thayer had no intention of boarding a boat. He stuck with his friends George and Harry Widener and Charles Duane Williams. When all the boats were gone Colonel Gracie saw John Thayer looking "pale and determined" by the midship rail aft of Lifeboat 7 talking with George Widener. They may have moved towards the stern like so many other passengers and crew, because when Gracie returned a short while later they had gone.
John B. Thayer's body, if recovered, was never identified.