The protocol, which is expected to advance and expand economic cooperation, was signed at the Croatian Chamber of the Economy by its president Nadan Vidosevic and the president of the Jordanian Chamber of Trade, Haydar Murad, in the presence of the two countries' prime ministers.
Vidosevic said the Business Council would also help Jordan access the central European market via Croatia and Croatia access Jordan's region.
The protocol was signed as part of a visit Jordanian PM Faisal al Fayez is paying to Croatia since Wednesday. He is accompanied by numerous business people.
Murad said the visit represented the Jordanian government's intention to build as many bridges with Croatia as possible, to mutual interest.
He voiced confidence the establishment of the Business Council would mark the start of ties in trade, investment and commodity exchange, which he said was below expectations.
Murad said Jordan represented a "strong strategic gate for the reconstruction of Iraq in which we can work together".
Croatian PM Ivo Sanader urged business people to embark on concrete projects, saying an agreement on the avoidance of double taxation between the two countries was expected to be ready in a few months.
His Jordanian counterpart al Fayez said there was a lot of interest in strengthening cooperation, notably in trade and investment.