The State Department said yesterday that it has granted a temporary visa to Protestant militant Ian Paisley of Northern Ireland to attend the World Congress of Fundamentalists from July 29 to Aug. 9 at Bob Jones University in Greenville, S.C.

Paisley, who has visited the United States on several occasions, had his visa invalidated by the department in December, 1981, after members of Congress charged that he supported terrorism in the struggle between Protestants and Catholics in Northern Ireland and that he intended to foster his policies through political speeches and other activities in the United States.

At that time, the department cited the "divisive tone" of his statements and said that "Mr. Paisley's presence in the United States is prejudicial to the United States."

In early 1982, Paisley applied for a temporary visa to speak at Bob Jones University's annual Bible Conference. The department turned him down, saying it was still "gravely concerned" over his "inflammatory actions and statements."

Bob Jones Jr., chancellor of the fundamentalist institution, addressing the 1982 conference, said the visa denial was "nothing but Catholic bigotry." He labeled then-Secretary of State Alexander M. Haig Jr. "a tyrant of the worst sort, a monster in human flesh and a demon-possessed instrument to destroy America. Let's pray that God will remove him. God answers prayers."

In September, 1982, Paisley was given permission to attend the funeral of a friend in California. But another visa request this March was denied.

The State Department said yesterday that it handles visas on a "case-by-case basis" and that the visa just granted is good only for the July 29-Aug. 9 conference dates.

A department spokesman said he did not know what security arrangements were being made by Bob Jones University, or what would happen if Paisley sought to use the temporary visa to go elsewhere in the country and make political speeches or fund-raising appeals on behalf of his faction. However, he said that Paisley, in applying for the visa, said his visit would be religious in nature. "We're satisfied the purposes for which we granted the visa are the purposes for which it will be used," the government spokesman said.

Paisley, the head of the Free Presbyterian Church of Northern Ireland, has a long history of association with Bob Jones University. He was listed in one university bulletin as a member of its "cooperating board" and elsewhere as a member of the school's international board of trustees. Another report said he had an honorary degree from the university.

The State Department said yesterday Paisley is listed as co-chairman of the World Congress of Fundamentalists, which, sources said, is not an organization but a meeting convened by Bob Jones University. University officials were not available yesterday for comment.

Sources on Capitol Hill said yesterday that Paisley's admission might be used as a wedge by some American politicians to demand that Northern Irish Catholic militants also be allowed to enter, resulting in renewed fund-raising here to finance IRA terrorist activities in Ireland.