The two airlines - which are both fully owned by the Investment Corporation of Dubai (ICD) and share the same chairman, Sheikh Ahmed bin Saeed Al Maktoum - said they will use the partnership to scale up their operations and accelerate growth.
The tie-up will include co-ordinated scheduling and integrated collaboration to ensure a beneficial combination of the networks of each carrier, with increased feed and the possibility of opening new routes.
They are expected to reach 240 destinations and 380 aircraft by 2022, according to the announcement.
The agreement will also see alignment of frequent flyer loyalty programmes, providing benefits to customers of both airlines.
Emirates suffered a 70 percent drop in profit in the year ended March 31 as the low price of crude clipped growth in oil-based Persian Gulf economies, terrorist attacks hurt demand for travel and the company faced USA -imposed travel restrictions.
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Emirates and flydubai will also align airport systems and operations at their hub at Dubai International Airport, the world's busiest for international travel.
"Over the past years FlyDubai has gradually encroached on Emirates' market, both in terms of serving overlapping routes and upgrading its product by moving away from the strict low cost model", Pistik said. The current combined network comprises 216 destination points.
The partnership will be rolled out over the coming months, with the first enhanced code-sharing arrangements to come into effect during the final quarter of 2017.
The partnership is working to optimise the networks and schedules of both airlines, to open up new city-pair connections offering consumers greater choice.
Teams from Emirates and flydubai are now working on several initiatives spanning commercial, network planning, airport operations, customer journey, and frequent flyer programmes alignment.
Emirates, the largest airline in the Middle East, flies to 157 destinations with 259 planes, while low-priced airline Flydubai reaches 95 destinations with 58 planes.