The burger chain has also been left without bottled drinks across its 1,250 outlets in England, Scotland and Wales as the lorry driver shortage takes its toll.
A spokesman said the group is “working hard to return these items to the menu”.
He said: “Like most retailers, we are currently experiencing some supply chain issues, impacting the availability of a small number of products.
“Bottled drinks and milkshakes are temporarily unavailable in restaurants across England, Scotland and Wales.
“We apologise for any inconvenience, and thank our customers for their continued patience.”
The group is understood to have temporarily halted selling milkshakes and bottled drinks to ensure supply across its broader menu in the face of the haulage and supply chain troubles.
McDonald’s is the latest to be hit by supply woes after Nando’s was last week forced to shut around 50 restaurants amid a chicken shortage. It blamed staffing shortages at suppliers and a reduced number of lorry drivers.
Rival KFC also warned recently that supply chain issues meant it was unable to stock some menu items.
Firms across a raft of sectors in the UK have been battling with a supply chain crisis due to a shortage of lorry drivers following post-Brexit EU immigration rules, Covid-19 restrictions and self-isolation rules.
The supply pressures have also been affecting supermarkets in recent weeks, while manufacturers have reported sharp increases in the prices of raw materials.
Business groups representing the retail and transport sectors have been calling for the Government to review plans not to grant temporary work visas to drivers from the EU.