Khaled Elbalshy, editor-in-chief of the news website Darb, which is banned in Egypt, was elected with 2,450 votes out of 5,062 cast, the union said.
"It's a breath of hope," Lina Attalah, editor-in-chief of Mada Masr, an online newspaper that is also one of hundreds of news sites blocked by the authorities, said on Twitter.
In a country where "there is no real representation resulting from elections, parliamentary or presidential for example, at the union level, there is no one who can represent us better than Khaled Elbalshy," she wrote, while three of her journalists are soon to be tried for "insulting" MPs.
Mr. Elbalshy had been at the forefront of a rare mobilization in May 2016. Police then carried out an unprecedented raid on the press union, arresting two reporters wanted for "inciting protests" against the authorities.
Hundreds of journalists had demonstrated to demand the dismissal of the Minister of the Interior and denounce a regime in "war against journalism".
The president of the union and two of his staff, including Mr. Elbalshy, then head of the union's civil liberties committee, had been taken into custody for sheltering the two wanted reporters.
"This is a historic day for Egyptian journalists, Khaled Elbalshy got more votes than the candidate promoted by the state despite all his support," tweeted journalist Rasha Azzab.
The Dostour party, one of the last voices of the liberal opposition, hailed an election that embodies "the hope for change after years of suffocating under a monopoly".
For Reporters Without Borders (RSF), "pluralism (of the media) is almost zero in Egypt, one of the largest prisons in the world for journalists" with currently, according to the NGO, 23 reporters behind bars, after conviction or in pre-trial detention.
Egypt is ranked 168th out of 180 countries in RSF's 2022 press freedom index, after falling nearly ten places since President Abdel Fattah al-Sisi took power in 2013.
© 2023 AFP