The 45-year-old former England international was appointed on a seven-month deal in November and led the team to five wins and four draws during his tenure.
However, Barnes has been told he will not be offered a new contract by the Jamaican Football Federation at the end of June, and is now expected to take the reins at English League One side Tranmere Rovers, whose roster includes Jamaican central defender Ian Goodison.
"Yes, I am disappointed that I would not be going to the Gold Cup [in July] because I could have started the contract [with Tranmere] after the Gold Cup," Barnes said.
"But I fully accept and understand the JFF decision that they will appoint Theodore, as of now, to give him a chance to experience football at the highest level.
"I have to thank the JFF for giving me an opportunity in doing something I love. It is something I wanted to get involved with for a long time and they gave me that opportunity," he said.
Jamaica's next major test comes next month in the CONCACAF Gold Cup to be played in the United States and featuring top regional squads now playing in 2010 FIFA World Cup South Africa™ qualifiers.
There had been great disappointment from the Jamaican Football Federation last year that the Reggae Boyz had failed to advance to the final round of FIFA World Cup qualifying. Jamaica beat Panama 3-2 in an international friendly last night.