Since taking power in a coup in 2022, the junta has suspended multiple TV and radio stations and expelled foreign correspondents, especially from French media.
Founded in 1960 and based in France, Jeune Afrique is a website and monthly magazine with several correspondents and contributors in Africa and elsewhere.
The government in Ouagadougou has suspended "all Jeune Afrique distribution media in Burkina Faso until further notice," its spokesman and communications minister Rimtalba Jean-Emmanuel Ouedraogo said in a statement.
He blamed "a new and misleading article... titled 'Tensions persist in Burkina Faso army' and published on Monday."
FILE - Supporters of Capt. Ibrahim Traore protest against France and the West African regional bloc known as ECOWAS in the streets of Ouagadougou, Burkina Faso, Oct. 4, 2022.
"This publication follows an earlier article by the same newspaper on the same website," published on Thursday, "in which Jeune Afrique alleged that 'Discontent is growing in Burkina Faso barracks,'" the statement added.
"These deliberate assertions, made without the slightest hint of proof, have no other purpose than to discredit the national armed forces and, by extension, all fighting forces in an unacceptable manner."
Some people interviewed by AFP in Ouagadougou still had access to the website, while others said they had problems connecting.
- Anti-France sentiment -
The decision came almost a year after Captain Ibrahim Traore came to power in a coup, the landlocked country's second in eight months.
In June, Burkina Faso authorities announced the suspension of the French television channel LCI for three months, after expelling the correspondents of the French dailies Liberation and Le Monde in April.
At the end of March, they had ordered the suspension of the television channel France 24.
Since 2015, Burkina Faso has faced recurring jihadist violence, which has left more than 17,000 people dead and more than two million internally displaced.
FILE - Russia's President Vladimir Putin and Burkina Faso's interim President Ibrahim Traore meet following the Russia-Africa summit in Saint Petersburg, Russia, July 29, 2023.
The two coups of 2022 were each triggered in part by discontent at failures to stem a raging jihadist insurgency.
Regional instability has also fueled recent military takeovers in neighboring Mali and Niger.
The succession of coups in the Sahel region has alarmed Western governments, as well as the Economic Community of West African States.
Anti-Paris sentiment has been inflamed in the three countries — all former French colonies — with military rulers strengthening ties with Russia.
Earlier this month, the juntas of Burkina Faso, Mali and Niger signed a mutual defense pact, to "establish an architecture of collective defense and mutual assistance for the benefit of our populations."
France withdrew its troops and ambassador from Burkina Faso earlier this year in the face of post-coup hostility.
Junta chief Traore this month gave an interview saying Burkina was not "the enemy of the French people" but of the policies of its government.
"We have to accept seeing each other as equals... and accept an overhaul of our entire cooperation," he told state television.