But despite the worldwide attention brought by his case, he died exactly one week short of his first birthday.
Francis wrote in a heartfelt message on social media, "I entrust little Charlie to the Father and pray for his parents and all those who loved him". The parents of the 11-month old, who has a rare genetic condition and brain damage, are returning to court Monday for the latest stage in their effort to seek permission to take the child to the United States for medical treatment.
However, several courts ruled that Great Ormond Street hospital was fitted to decide whether the baby had a chance of survival, and they had a legal obligation to decide when to disconnect Charlie from life support.
Hundreds of people in the United Kingdom who called themselves "Charlie's Army" supported his parents and raised £1.35 million ($1.77m) for them to take him to the US for treatment.
Prime Minister Theresa May said she was "deeply saddened" and extended thoughts and prayers to Charlie's parents, according to BBC News. "My thoughts and prayers with Charlie's parents Chris and Connie at this hard time".
"We are so proud of you, Charlie", his mother Yates said in a statement.
Britain's courts, after hearing a wealth of medical evidence, ruled that it would go against Charlie's best interests to have the experimental nucleoside therapy advocated by a US professor of neurology, Michio Hirano. This was upheld by a British Supreme Court decision that the hospital could discontinue life support to Charlie and he could not be transferred to the U.S. or elsewhere.
On Thursday, with the hospital and Charlie's parents still at an impasse, the judge's order to remove life support and move Charlie to hospice took effect.
The European Court of Human Rights refused to intervene in the case.
The death of baby Charlie Gard last night following a bitter court battle has drawn prayers and commiserations from around the world.
Alison Smith-Squire, a journalist and spokeswoman for Charlie's parents, defended their decision to go for publicity.
A spokesman for Great Ormond Street Hospital said the facility "had tried absolutely everything" to accommodate the couple's wishes, but added that "the risk of an unplanned and chaotic end to Charlie's life (would have been) an unthinkable outcome for all concerned". "Sometimes they do not have the strength, confidence or support to deal with the media and the public and often find themselves under pressure to agree with the hospital over a course of action". The Holy Father's statement said he was "following with affection and sadness the case of little Charlie Gard and expresses his closeness to his parents".
His plight drew sympathy from US President Donald Trump, who tweeted on July 3 that the US would "be delighted to help".
Great Ormond Street soon reported that its doctors and nurses were receiving serious threats over the case. "Sweet dreams baby. Sleep tight our handsome little boy'".
They asked him to let them take Charlie home so that they could spend the final days with their son.