It will close to all traffic at 20:00 GMT and reopen 48 hours later, each weekend until 19 December.
During the works, about 50,000 tonnes of material will be laid on the 2.9km (1.8 mile) runway.
Traditionally, airports close for up to 14 days to carry out such work.
Airport bosses said completing the refurbishment over several weekends rather than all at once was the "best way to avoid major disruption".
The closures were agreed following two years of discussions with retailers and airlines, airport management added.
"Some of our retail partners are refurbishing their shops which they wouldn't be able to do when the airport is open," said Jack Kelly from EMA.
"We've made sure flights can come in ahead of the closure and more flights can go out after it, so we are limiting the amount of disruption."
The runway was last refurbished in 1999 and has a lifespan between 12 to 17 years.
Engineers will also be replacing 1,200 lights around the runway with LEDs.
The runway will be divided up into seven sections, with one chunk being repaired and sealed off each weekend.

Liberty, headed by Sanjeev Gupta, was first to express an interest in the assets when they were put up for sale.
A spokesman for Liberty told the BBC that the firm had put together a team of advisers and financial backers.
"The formal process is to submit a letter of intent; it amounts to a bid. It will be done on Tuesday," he said.
In addition to the Port Talbot factory - the UK's largest steelworks - Tata's remaining assets include sites at Newport, where more than 1,300 people are employed, and Rotherham, which employs 1,200. Tata also has operations at Corby, Shotton and Teesside.
Macquarie, the Australian bank, was advising Liberty on a potential bid, and is considered a potential financial backer of any takeover.
Liberty House started life in the university room of Indian-born founder Sanjeev Gupta.
While a student at Cambridge University in 1992, the budding entrepreneur started what has since become a global steel and commodities business with annual sales of more than £2bn.
With operations in 30 countries, and headquarters in London, Dubai, and Singapore, Mr Gupta's Liberty has also emerged as a possible saviour of Britain's steel industry.
Liberty's focus is on recycling the mountains of scrap metal generated in the UK, rather than the historical method of producing steel in blast furnaces.
Last month, it acquired Tata Steel's plants in Lanarkshire. In recent years, it has reached similar deals for steel plants in Newport and the Black Country.
A management buyout team is also planning to submit a bid under the name Excalibur Steel UK Limited.
It has appointed investment banker Mark Rhydderch-Roberts as a non-executive director. He joins Stuart Wilkie, the head of Tata's United Kingdom strip steel business, and former Alcan senior executive and venture capitalist Roger Maggs, on the board.
The government has promised to support any buyer of the business by taking up to a 25% stake in a new business and making hundreds of millions of pounds of finance available.
Tata has not publicly set a deadline for any deal, but has made it clear it cannot sustain its £1m-a-day losses indefinitely and does not want to prolong the uncertainty for workers and customers.
Tata's Scunthorpe operation, which employs more than 3,000 people, has been sold to investment firm Greybull Capital for a nominal £1.
East Midlands Airport (EMA) will shut later for the first of seven consecutive weekends to resurface the runway - a first for a UK airport, bosses have said.
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Liberty House plans to submit a formal bid on Tuesday to buy Tata Steel's UK assets, which include the Port Talbot works employing about 4,000 people.