The site went down after customers rushed to buy this week's "Star Gift," a weekly offer on some of the retailer's Christmas gift sets.
Earlier there was a holding message on the website that says the site has crashed because "so many of you are shopping our amazing deals".
Boots say the website is now back up but it places customers in a virtual queue before they can enter the site.
It's thought the outage was caused partly by today's new "Star Gift" offer on two No 7 gift sets.
Shoppers flocked to buy the better-than-half-price gifts but the volume of traffic crashed the website and kicked customers off.
Sales tracking website LovetheSales estimates the website is losing £1.52 million sales an hour because of the crash.
People took to Twitter to say they're furious that the website has gone down with just 11 days to go until Christmas as they scramble for last-minute gifts.
One wrote: "Really really annoyed that such a large company like @BootsUK @BootsHelp website is down yet they have not released an update as to when will be back up & running."
Another said: "@BootsUK website down on the second busiest Friday of the year?? Come on Boots."
A shopper also tweeted: "Website has been down for 4 hours. Shocking on such a critical day."
Boots released two Star Gifts today: A No7 Collection Gift Set reduced from £80 to £39, and a No7 Men Ultimate Supercharged Collection reduced to £20 from £42.
They will be available at a reduced price until Christmas Eve in stores and online – once the website starts working again.
Boots says that the contents of its No7 Collection Gift Set are worth £149.50.
A Boots spokeswoman said shoppers keen to get their hands on today's Star Gifts can still pick them up in store.
She added: "We are sorry to say we are currently experiencing some technical issues on Boots.com.
"We really appreciate our customer’s patience as we work hard to get back up and running as quickly as possible."
Today is set to be one of the busiest Christmas shopping days of the year as people finish their present buying.
Meanwhile with less than two weeks to go until the big day, Tesco has slashed the cost of Christmas veggies to only 29p each.
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