Footage showed the Labour Party leader arriving at Glasgow Central Station, where a group of activists were waiting with Palestinian flags.
Sir Keir voted against a ceasefire in Gaza and has lost many councillors from mainly Muslim communities due to his support for Israel during a war which has killed more than 16,500 Palestinians.
The backlash began during an interview with LBC where he claimed “Israel has the right” to withhold power and water from Palestinian civilians.
The majority of victims have been women and children, and starvation and water-borne illnesses are now becoming widespread in makeshift camps.
As Sir Keir arrived, one protester shouted: “Keir Starmer you are facilitating Israel’s genocide in Gaza. Stop the massacre of over 7,000 babies.
“Freedom for Palestine, stop the genocide. You’re responsible for killing babies in Gaza.”
Another shouted: “Starmer, why did you vote for continued genocide?”
Others said: “War criminal” and “You should be in prison”.
After Sir Keir got into a Range Rover, activists surrounded it shouting “child murderer”.
The protest continued outside the Crowne Plaza, where Scottish Labour leader Anas Sarwar also came in for criticism from protesters “for supporting genocide”.
Footage filmed on a train earlier, showed a passenger confronting Sir Keir over the “slaughter” of 7,000 Palestinian children.
The passenger can be seen saying: “Keir, how many more children in Palestine have to die before you call for a ceasefire?
“Over 7,000 children have died. Over 7,000 children have been slaughtered by Israel. This is unacceptable.
“What happened to human rights? What happened to democracy?”.
The man goes on to say “20,000 people have died”, and asks: “Where is your humanity?”.
A Police Scotland spokesperson: “We are aware of an ongoing protest at a premises on Congress Road, Glasgow, and an earlier protest in the Gordon Street area of the city.
“Officers are in attendance at Congress Road and engaging with the crowd.
“Two people have been arrested in connection with assaulting police officers at Congress Road and inquiries are ongoing.
“There have been no reports of any injuries at either protest.”
