Development of the R-99 began during the 1990s in response to a FAB requirement for an airborne early warning and control (AEW&C) platform, as well for the export market.

It has been deployed in response to various events, including the Shining Path hostage crisis, the loss of Air France Flight 447, the 2011 military intervention in Libya, and the SIVAM program.

During the 2010s, the FAB opted to modernise their R-99 fleet, not only extending its service life but also giving it new capabilities, such as a longer effective radar range and datalink facilities.

Embraer has proposed new variants of the type, such as the armed P-99 anti-submarine warfare (ASW), which is to be capable of using both torpedoes and anti-ship missiles.

During the aircraft's development, particular attention was paid to market interest as well the specific requirements of the Brazilian Air Force (FAB).

[5][6] The P-99 would be the anti-submarine warfare (ASW) modification of the EMB 145 MP and would have four underwing hardpoints, which could be mounted with a variety of torpedoes and/or anti-ship missiles.

[8] During September 2003, a Brazilian R-99 was deployed on request of Peruvian authorities to locate the site where 71 hostages were being kept by the armed group Shining Path.

The R-99 synthetic-aperture radar allowed to locate — even at night and under bad weather conditions — aircraft's debris and victims bodies 800 km away from Fernando de Noronha Archipelago.

[23][24] During 2022, during the Russian invasion of Ukraine, Hellenic EMB-145H's flew several daily combat missions, monitoring NATO allied airspace over Romania and Bulgaria while covering part of the Black Sea.