The aid decision reflects the new tenor of American foreign policy under Mr. Pompeo and the national security adviser, John R. Bolton, who have shown a willingness to trade American leadership on human rights for an embrace of friendly autocrats like Mr. Sisi who share their hostility toward political Islam.

Mr. Sisi has long enjoyed a warm relationship with President Trump, who hailed the Egyptian leader as a “fantastic guy” and even publicly complimented his taste in shoes. But the Egyptian leader had a tougher time from the previous secretary of state, Rex W. Tillerson, who last August denied Egypt $96 million in aid and suspended $195 million.

Egyptian officials were shocked at the rebuke from the United States, which over the past 40 years has given Egypt $47 billion in military aid and $24 billion in economic assistance. Mr. Tillerson was said to be angry that Mr. Sisi had broken a private promise, made in Washington, that he would not sign the harsh law on aid agency regulations. In May 2017, Mr. Sisi went ahead and enacted the law anyway.

Mr. Tillerson also sought to press Egypt over its relationship with North Korea, which operates a large embassy in Cairo that it uses to carry out illicit arms sales across the Middle East, according to United Nations inspectors.

Mr. Sisi’s government has partly addressed some American concerns. A retrial of the case involving the 43 foreign aid workers, many of whom were convicted in absentia, is scheduled to start this year. Egyptian media reports say that Mr. Sisi has forced North Korea to cut the number of diplomats stationed at its embassy in Cairo.

But such restrictions can be easily circumvented through the use of accounting measures, like counting diplomats as spouses, said Mr. Miller, the analyst, who worked on Egypt at the State Department until last year. “If past is prologue, we will see that as soon as the U.S. looks the other way, the Egyptians will start up their relationship with North Korea again,” he said.

On most other fronts, things have gotten markedly worse in Egypt. Since Mr. Sisi’s re-election in May, after a carefully managed vote, the president has redoubled his efforts to lock up even relatively mild critics.