The government says the temporary measure will help ensure more women can access the medication amidst shortages.
The three month supply limit applies to Oestrogel, Ovestin cream and some Premique tablets.
Meanwhile the government has appointed a new HRT Tzar whose job is to help solve the crisis.
There are rising concerns about shortages of HRT across the UK.
Women unable to obtain their choice of medication have experienced symptoms including migraines, severe backpain and hot flushes.
Officials say there are alternative HRT products that may be a suitable swap for some.
The government says the limits will even out the distribution of in-demand products which have recently experienced supply issues due to rising demand.
Women who have a prescription for more than three months but are only able to access three months' supply will not have to pay an additional prescription charge, the government has confirmed.
Madeline McTernan, the new HRT Tzar, said: "This is a step in the right direction of tackling the supply issues women are facing when it comes to accessing HRT and ensuring ongoing, reliable supply."
Health and Social Care Secretary, Sajid Javid, said he wanted to reassure women that the had listened to their concerns and "would not hesitate to take decisive action to ensure they had access to the HRT they need".
"We will leave no stone unturned in our national mission to boost supply of HRT - and this next step will ensure women across the UK will be able to reliably access this vital medication and maintain this lifeline for millions who need it," he said.
Demand for HRT has risen with a 38% increase in the number of prescription items over the last seven years, according to the Department for Health and Social Care.
Officials say anyone who is worried about access to HRT should speak to their doctor.