King Salman's Middle East kingdom banned the Arabic edition, whose front showed the pontiff standing in the Sistine Chapel.
There has not yet been any official statement from the Saudi government spelling out its cultural opposition to the magazine, but its regional editor-in-chief, Alsaad Omar Al Menhaly made the puzzling announcement on Twitter.
It read: "Dear readers in Saudi Arabia, we apologize for you not obtaining August’s magazine. According to the publishing company, the magazine was denied entry for cultural reasons. Chief Editor" (sic)
The cover story addresses Pope Francis' "silent revolution" and hopes to create a church "that is poor and for the poor".
From his bold pronouncements on climate change and divorce, to his recent call for parishes and dignitaries to take in Syrian refugees, some see Pope Francis as a revolutionary.
The very act of putting the Vicar of Christ on the cover would have been controversial enough for senior officials of a country where the mosque and state are so closely entwined.
But Saudi officials may have been rattled by the Pope's groundbreaking reforms of his church, given the strict rigidity of the Wahhabi state.
Wahhabi, members of the strictly orthodox Sunni Muslim sector, advocate a return to early Islam and a literal interpretation of the Koran.
It is not the first time the magazine has been censored in King Salmon's Middle East kingdom.
Earlier this year, a line in the magazine's 'War on Science' March issue stated "evolution never happened". This was emitted from the magazine's front cover for unknown reasons.
Kacem El Ghazzali, a secular activist from Morocco who is currently serving as International Humanist and Ethical Union‘s representative at the United Nations, said it was fairly common for scores of “scientific, secular, and philosophical” to be banned in the oil-rich kingdom.
He added: "Thousands of blogs and websites are also banned in the country and contrary to most Arab countries, Saudi Arabia never tries to hide its intentions and recognition of censorship.”
A spokesperson for the National Geographic Society said: “We are aware of the issue, but we are still currently in the information gathering phase.”