Emirates in particular has been hit by currency fluctuations, geopolitical uncertainty and U.S. travel restrictions leading it to post an 82 percent drop in profit in May, its first decline in five years.
While continuing to be managed independently, the airlines will leverage each other's network to scale up operations and accelerate growth.
"The partnership will strengthen the position of both airlines and allow them to optimize use of their respective fleets with a greater ability to adjust aircraft capacity size according to route demand", said John Strickland, aviation industry consultant at JLS Consulting.
Emirates cited fierce competition and a "relentless rise" in the U.S. dollar as the main factor in falling revenues.
Flydubai passengers will have "seamless connectivity" to the Emirates long-haul network, while Emirates says it will benefit from the low-priced operator's regional service.
The partnership will go "beyond code-sharing and include integrated network collaboration with coordinated scheduling", said the carrier.
Working together on a number of initiatives spanning commercial, network planning, airport operations, customer journey, and frequent flyer programme alignment, the two carriers are expected to reach 240 destinations served by a combined fleet by 2022.
The partnership will also mean greater integration between the airlines' existing hubs at Dubai International, where Emirates now operates from its own dedicated Terminal 3, and flydubai mainly operates from Terminal 2.
Meanwhile flydubai, which operates 58 Boeing 737 aircraft to 95 destinations, has focused mainly on regional destinations throughout the Middle East, India, Southern Europe and Eastern Africa.
"Both airlines have grown independently and successfully over the years and this new partnership will unlock the vast value that the complementary models of both companies can bring to consumers, each airline and to Dubai".
The airline's networks overlap to an extent but, between them, the carriers operate to 216 cities.
The partnership will be rolled out over the coming months and start with code-sharing arrangements in the last quarter of 2017.