Media reports identified the victim as six year old Zakariya Bader al-Jabir from Jeddah who was on a pilgrimage to the holy city with his Shia mother, fueling speculations that there could be sectarian motive behind the crime.
The New Arab website says his mother's recitation of salutations for the family of Prophet Mohammed (Pbuh) outraged the taxi driver who, according to "witnesses", broke a glass bottle, before grabbing the boy by the back of his shirt and slitting his throat in front of his mother.
The Muslim Vibe website's account is also similar to that of the New Arab. It says the mother and the child had taken a taxi on their way to al-Masjid al-Nabawi Mosque in the middle of the day, when the driver "pulled over the car, got out, and forced the boy out of the car near a coffee shop in the al-Tilal neighborhood."
"The taxi driver then broke a glass bottle to obtain a shard of glass, which he then used to cut the throat of the child and stab him," the report said.
His traumatised mum tried to stop the driver from killing her boy, and collapsed on the street.
Passers-by told TMV that a cop stationed nearby also tried to stop the man from attacking the boy, but he was unable to save the child.
However a Washington based rights group issued a press release saying that the "unknown man" had asked the mother if she was Shia when they arrived at the shrine, and "the woman said 'yes'."
"Minutes after this conversation", the child was wrenched away from her and attacked with a broken piece of glass, The Sun, London reported
The group added: "Witnesses report the child was beheaded from behind his head as his mother watched and screamed.
"There was no intervention from anyone and no response from authority thus far."
Saudi Shia community "came together in mourning and to show solidarity with the parents, the report said.
Videos went viral, purportedly showing the body of the little boy in a mosque, where a local cleric Sheikh Amri is mourning his death and making a speech to a group of people gathered around the body.
"This young child reminds us of Karbala. Zakariya is also the victim of Harmala. May Allah grant him paradise with the infant of Imam Hussein," the cleric is heard saying in one video, referring to the story of the martyrdom of third Shia Imam, Hussein ibn Ali, and his family members, including his infant Ali-Asghar, in Karbala.
Semi official Saudi Gazette also reported the incident. The report however mentioned that the 35-year-old assailant was sitting in the coffee shop and went out when he saw the young boy walking in front of him with his mother.
"The killer quickly grabbed the boy from the hands of his mother, broke a bottle he found near the coffee shop and stabbed him," the report said.
The boy had ordered a meal from a nearby restaurant and was going to collect it when the man saw him. The mother fought desperately to save her son while screaming for help from people who were passing by.
A policeman, who happened to be at the scene, unsuccessfully tried to save the child from the grip of the man.
"He, however, was able to overpower him after his atrocious act before more officers arrived at the scene," the report said.
The report mentioned that the mother, a heart patient working in Jeddah had come to Madinah with her son to pray at the Prophet Muhammad's (SAW) Mosque.
"The mother was in complete shock and was taken to a hospital," the report said.
The Madinah police opened an investigation into the incident, which has baffled the residents of the holy city.
The fact that the mother and child were part of the marginalized and minority Shia group of Saudi Arabia, and the fact that Saudi Arabia has an awful humans rights record has raised questions about this case.
In 2016 the Saudi authorities executed Shia cleric Sheikh Al Nimr and the 2018 murder of journalist Jamal Khashoggi (and subsequent failed attempt at covering their tracks), also points to a wider issue of persecution, underreporting and suppression within the Kingdom.
No official statement has been issued by either the police department or Saudi Arabia as of now over the potential link to sectarianism in this investigation.