The song, which features in the Despicable Me II film, is starting a fourth non-consecutive week at number one.
This impressive run means Pharrell is only the third act in history to hit number one on three separate occasions with the same song - and the first in 57 years to achieve this feat, said the Official Charts Company.
The other two to reach the top three times were Frankie Laine with I Believe in 1953 and Guy Mitchell with Singing The Blues in 1957.
When Happy passed one million sales this week, Pharrell joined The Beatles as the only acts to score three million-sellers in 12 months. His collaboration with Daft Punk, Get Lucky, passed the million mark in June 2013 and his chart-topper with Robin Thicke and T.I., Blurred Lines, passed the landmark the following month.
Pharrell is only the third act to notch up three million-selling singles in the UK. The Beatles have six altogether, and Rihanna three.
He told OfficialCharts.com: "I am beyond grateful for the amount of love and support I've received in response to Happy - it is overwhelming. I've always respected the great taste of the UK, and I'm honoured to have my music embraced in such a positive way. I am so thankful."
Last week's chart-topper from Sam Smith, Money On My Mind, slips to number two. Clean Bandit's Rather Be, featuring Jess Glynne, another former number one, is a non-mover at number three. Katy Perry's Dark Horse climbs two places to number four and A Great Big World featuring Christina Aguilera fall one place with Say Something to complete the top five.
In the album chart, Bastille's debut collection Bad Blood retains the top spot by just over 1,000 copies.
The winners of Best British Breakthrough at the Brit Awards last month overtook midweek leader Beck to hang on to number one, just 1,000 copies ahead of fellow Brit winners Arctic Monkeys, whose Mastercard Album of the Year AM had to settle for second place. Ellie Goulding's Halcyon climbed one place to number three.
Beck, who was out in front by a mere 450 copies on Wednesday's chart update, finally landed at number four with Morning Phase. He may have been denied a chart-topping album, but his position is still a personal best - his previous high in the album chart was a number nine with Modern Guilt in 2011.
Beyonce's self-titled album advances two more places to return to the top five.