Police were called just minutes apart to the shootings at two locations in close proximity in High Street, Wealdstone.
Both boys have been taken to hospital and Scotland Yard said they await details of their condition.
Officers were called to High Street at 1.17pm on Sunday to find a 15-year-old boy had been shot.
Two minutes later they were alerted by London Ambulance Service about a second victim, aged 12, who had been shot at a different location nearby.
Police said they are investigating whether the two incidents are linked.
No-one has been arrested and no firearm has been recovered.
The news of the shooting comes just hours after a 17-yearold was shot dead near his home in south London.
Rhyhiem Ainsworth Barton was discovered with critical injuries on Warham Street in Southwark on Saturday evening.