In typical Charlie Hebdo fashion, the special edition features a bloodstained, bearded God-figure in sandals with a Kalashnikov slung over his shoulder under the headline: "One year on: the killer is still at large."
The Vatican criticised the cover for failing to "acknowledge or to respect believers' faith in God, regardless of the religion."
"Behind the deceptive flag of uncompromising secularism, the weekly is forgetting once more what religious leaders of every faith unceasingly repeat... using God to justify hatred -- is a genuine blasphemy, as Pope Francis has said several times."
The provocative cover is typical of the fiercely-secular publication whose drawings of the Prophet Mohammed drew the fury of Muslims around the world and inspired the bloody attack on its offices on January 7th last year.
Eight Charlie staff were gunned down by brothers Said and Cherif Kouachi as well as several others in and around the building in the assault, which kickstarted three days of terror in the French capital that would eventually leave 17 dead.
The bloodshed stunned a nation that has become a prized target of jihadists and was again plunged into grief in November when 130 people were killed in coordinated attacks around Paris.
'Shake up people's ideas'
The attack on Charlie, as well as a Jewish supermarket and police, brought millions into the streets in protest and led to much soul-searching over the country's cherished secularism as well as societal issues such as integration.
"It was unthinkable that in France in the 21st century, journalists would be killed by religion," cartoonist Riss, who lost the use of his right arm in the attack, wrote in the editorial of the special edition.
"We saw France as an island of secularism, where it was possible to tell jokes, draw, laugh, without worrying about dogma, fanatics."
In an interview with AFP, he said that with the latest cover, which he drew, he "wanted to go above one religion or another."
"It is the idea of God itself that we, at Charlie, contest. You need to shake up people's ideas or they stay stuck in their positions."
The special edition devotes several pages to the topic of secularism, as well as reflections on the terrifying minutes when the Kouachi brothers burst into an editorial meeting spraying gunfire.
In one article on secularism, a cartoon depicts a masked gunman saying: "First kill those who do not pray, it will convince the others that God exists."
In his editorial Riss, wrote that the team was keenly aware of the fact that since publishing images of the Prophet Mohammed, seen as forbidden by many Muslims, "many hoped someone would one day put us in our places."
The attack, claimed by Al-Qaeda's branch in the Arabian Peninsula, was not the first on the publication, which was firebombed in 2011.
He said the Charlie team had often thought of death -- albeit the economic kind -- as the weekly constantly flirted with financial ruin with circulation hovering at 30,000.
Ironically, the attack made it one of the best known publications in the world with the hashtag #JeSuisCharlie sweeping the Twitterverse and sales of 7.5 million copies the week after.
'Two idiots in balaclavas'
And Charlie has continued to raise ire, refusing self-censorship in the wake of the attacks, working from ultra-secure offices in a top-secret location.
When Riss pictured Aylan Kurdi, the Syrian toddler found dead on a Turkish beach this year, under a McDonald's sign in what was intended to be criticism of the consumer society, he was accused of racism.
The cartoonist said in his editorial he was often asked how he managed to continue after what had happened.
"We want to beat the crap out of those who wanted us to die more than ever.
"It is not two little idiots in balaclavas who are going to screw up our life's work. It is not they who will kill Charlie, it is Charlie who will see them die."
However those killed are never far from the minds of the cartoonists.
"I ask myself sometimes if I am making the newspaper they would have made. To me, they are no longer there but they are not gone."