The former England and Middlesbrough manager has stepped down after their 0-0 draw with Curacao in their final World Cup qualifier.
The result sees Curacao reach the World Cup, while Jamaica miss out on qualifying.
McClaren, who took the job after being part of Erik ten Hag's staff at Manchester United, said: "Over the last 18 months I have given everything I have to this job," he said. "Leading this team has been one of the greatest honours of my career.
"But football is a results business and tonight we have fallen short of our goal, which was to qualify from this group.
"It is the responsibility of the leader to step forward, take accountability and make decisions in the best interests of the team.
"After deep reflection and an honest assessment of where we are and where we need to go, I have decided to step down as head coach of the Jamaican national team.
"Sometimes the best thing a leader can do is to recognise when a fresh voice, new energy and a different perspective is required to move this team forward."