After a marathon meeting, the Prince George's County Board of Education voted early yesterday to cut a total of 550 jobs of various kinds, eliminate junior high school inter-scholastic sports and make other economies to accommodate a $10 million budget cut.

The votes came at a grueling, six-hour session at which the board attempted to make as few changes as possible in class size, school transportation and teacher strength.

Although 550 positions were eliminated, most of the persons who hold those jobs will still be employed by the school system although some may have to take a pay cut. Some teachers will be shifted to a new substitute teaching pool to preserve their employment.

Most of the steps finally agreed to at the meeting had already been under discussion in recent weeks as the board sought ways to accommodate the County Council's $10 million cut in the board's $288 million budget request for the next school year.

The budget cutting was necessitated by tax revenue limits imposed by TRIM, the county charter amendment approved by the voters last fall.

"You are trying to get on the good side of all the issues," board member A. James Golato told his colleagues as they discussed whether to fund special education transportation or elementary school guidance counseling.

One impact of the cuts will be larger classes in most schools because of the loss of 110 teachers and other professionals.

School officials said the consequences of the budget reduction will also be manifest in reduced maintenance and other services at school buildings. They warned that fuel and utility costs are rising and that maintenance budgets are already cut to the bone.

The cuts also included 35 of 116 planned replacement school buses, funds for bus transportation for special education in the summer of 1981 and a 5 percent across-the-board reduction in spending for office supplies.

The budget still contains money to fund 5 percent raises for teachers, although County Executive Lawrence J. Hogan had sought to hold the raises to 3 percent.