Maurice Flanagan, who previously worked at British Airways, Gulf Air, and BOAC, was appointed chief executive officer of the new airline. To highlight the airline's early success, Gulf Air, during Emirates' first year of operations, suffered a 56% drop in profits, and a loss the following year. By 1986, the airline had added destinations such as Colombo, Dhaka, Amman and Cairo to its route network. In 1987, a second Boeing 727 was purchased from the Dubai Government and an A300 was temporarily replaced by a second example from Kuwait Airways.

On 3 July 1987, Emirates received its first bought aircraft, an Airbus A310 and with two examples, launched daily non-stop services to London Gatwick on 6 July the same year. The airline in 1987 added Frankfurt via Istanbul, and Malé (Maldive). By the end of 1987, Emirates was serving 11 destinations. This was followed by an expansion into the Far East market in 1989, with flights to Bangkok, Manila and Singapore and Hong Kong in 1991.

Emirates continued to expand during the late 1990s. The growing cargo business accounted for 16 percent of the airline's total revenues. Emirates started offering round-the-world services from autumn 1993, after a partnership was established with US Airways. By 1995, the airline expanded the fleet to six Airbus A300s and eight Airbus A310s and built the network up to cover 37 destinations in 30 countries.

In 1996, the airline received its first Boeing 777–200 aircraft, and was followed shortly thereafter by six Boeing 777-200ERs. The arrival of the 777s allowed Emirates to continue its Singapore service onward to Melbourne commencing in 1996. In 1998, Emirates Sky Cargo was launched. Although the Emirates had always provided a cargo service using capacity within its passenger aircraft, this was now expanded with an aircraft, crew, maintenance and insurance lease with Atlas Air, initially for a single Boeing 747–200 freighter.

In May 1998, Emirates paid the Government of Sri Lanka for a 43.6% stake in SriLankan Airlines Emirates subsequently sold its stake in the airline to the Government of Sri Lanka, that was finalised in 2010. In 2000, Emirates placed an order for twenty five Boeing 777-300s, eight Airbus A340- 500s, three Airbus A330-200s and twenty-two of the double-decker A380. The first A330-200 arrived in 1999 and leased A340-300 in 2003.

Its frequent flyer programme, Skywards, was also launched in 2000 as the airline grew. The financial year 2001–02 would prove to be very difficult for Emirates and one of the toughest for the airline. Initially sales were affected by a recession and later influenced by the bombing of Colombo Airport. The bombing destroyed three of SriLankan Airlines' twelve aircraft and damaged three other aircraft.

A few months later, the September 11 attacks in New York City saw thousands of cancellations and deferments of travel plans. The airline announced a recruitment freeze, but did not make any redundancies. The airline also reduced flight frequencies to other destinations. At the 2003 Paris Air Show, Emirates signed an order for 71 aircraft. The order included firm purchase orders for a further 21 Airbus A380-800s and lease orders for two A380- 800s.

In 2004, Emirates began flying non-stop to New York City's John F. Kennedy International Airport using its new Airbus A340-500. These flights meant the resumption of non-stop air services between the United Arab Emirates and the United States, after Delta Air Lines withdrew its flights.

In 2005, Emirates ordered 42 Boeing 777s, the largest Boeing 777 order in history. In 2007, the airline signed contracts for 120 Airbus A350s, 11 A380s and 12 Boeing 777-300ERs. Also in 2007 by opening flights to São Paulo in Brazil, Emirates began the first non-stop flight between the Middle East and South America.

Emirates, took delivery of the first A380-800 in August 2008 and flew its first revenue flight from Dubai to New York City-JFK. Emirates went on to be the largest carrier to operate the A380 with a total of 90 orders until 2010. Emirates announced it does not expect to retire early airframes before 2020.

In 2009, Emirates became the world’s largest operator of the Boeing 777 with the delivery of its 78th example of the type. In 2010, Emirates said it planned to operate over 120 Airbus A380s when new airport space is available. The target implied a future Emirates order for 30 A380s.

In 2010, at the Farnborough Airshow, the airline placed an order for 30 Boeing 777s. In 2011, again Emirates placed another order for another 50 777s. The growth of Emirates has drawn criticism from carriers such as Lufthansa and Air Canada, who claim Emirates has unfair advantages. Emirates has not been given more landing rights in Canada beyond Toronto, and has been denied expansion to Calgary and Vancouver. In Germany, it’s not able to fly to Berlin nor to Stuttgart due to the same landing rights.

On 6 September 2012, it was announced Emirates and Qantas had signed a 10-year agreement to set up a major alliance, which would see Qantas move its hub for its European flights from Singapore to Dubai International Airport and end its 17-year revenue-sharing agreement with British Airways on the services between Australia and Britain. Qantas began daily Airbus A380 services from both Sydney and Melbourne to London via Dubai, meaning that together the two airlines were providing 98 weekly flights between Australia and the Emirates hub. Qantas became the only other airline operating at Terminal 3 at Dubai International Airport.

At the 2013 Dubai Air Show, Emirates made aviation orders history with an order for 150 Boeing 777X and 50 Airbus A380 aircraft, bringing the overall order total to 140 A380's. The airline announced its plans to move all operations to Dubai World Central - Al Maktoum International Airport sometime after 2020.

On November 12, 2017, Emirates Airline agreed to buy a number of Boeing's 787 Dreamliners . With the first deliveries planned for 2022, the deal included 40 of the new 787-10, the largest available Dreamliner. On 18 January 2018, it was reported that Emirates had placed an order for 20 A380s with options for 16 more with deliveries to start in 2020.

In 2014, Emirates launches flights to Boston, its 8th gateway in the USA, it also becomes the first airline to offer a scheduled A380 service at London Gatwick. In 2016, Emirates introduces 6 new destinations in its global network Yangon, Hanoi, Yinchuan, Zhengzhou, Cebu and Clark.