- Putnam: "I don't care much for your excuses, gentlemen. We should be building on Bunker Hill. Breed's is closer to the city, but it is also closer to their artillery!"
- Prescott: "Our orders came from men so divorced from the situation, we are compelled by reason to employ our own faculties to make a proper determination."
- Putnam: "Were that I could understand even half that nonsense you just uttered."
- Prescott: "What's not to understand?! I'm trying to ensure our victory!"
- —William Prescott arguing with Israel Putnam, 1775.[src]
When it was discovered that British troops were planning to take Dorchester Heights and Charlestown during the Siege of Boston, Prescott was chosen to lead the rebels onto the Charlestown peninsula and build fortifications at Bunker Hill on the night of 16 June 1775. When he arrived, he chose to build the fortifications at Breed's Hill instead.
Breed's Hill was closer to Boston than Bunker Hill, making it easier to fire artillery at the city. However, it was also easier for the British forces in Boston to fire back. It is possible that Prescott failed to notice the vulnerability of the position, since the fortifications were built in the dark of the night. As the Battle of Bunker Hill broke out the following day, Prescott and the commanders argued with General Israel Putnam over the site of the fortifications.
Although the rebels were eventually forced to retreat, the British lost many of their men, including officers. Thanks to Prescott, the rebel troops remained well-disciplined, proving their worth against the British Army.