Originally designed for military use in the Second Polish Republic in 1937, it was not opened by Polish authorities. Instead, it was made operational during World War II in 1940 as an airbase by the German Luftwaffe in occupied Poland. Postwar, between 1945 and 2000 it was used by Polish and Soviet air forces. In 2000 the Polish Ministry of National Defence declared the airfield closed. Before development, the airport featured one asphalt runway 2,500 m long and 60 m wide at an elevation of 104 m. The runway was in poor condition and lacked proper lighting and modern radio navigation aids such as an Instrument Landing System.
Subsequently, much of its original area was made available as capital in a joint management limited liability company created to run the future airport, Port Lotniczy Mazowsze Warszawa-Modlin Sp. z o.o. The airport was converted for civilian use, primarily as a replacement for the now closed Etiuda terminal for low-cost carriers at Warsaw's main Chopin Airport, this idea emerged in the early 2000s. Numerous projected opening dates had slipped, and business plans with extensive infrastructure improvements, including a new passenger terminal, had been proposed without any actual progress in the construction for some time. An environmental assessment was completed as well. A schedule, announced in February 2008 had the airport opening for business in early 2010. On 8 February 2010, the airport was registered officially as a civil airport by the Polish Aviation Authority (Urząd Lotnictwa Cywilnego).
In September 2009 it was announced that tenders were being accepted and funding had been secured from the EU for an opening in 2011, in time for the Euro 2012 Football Tournament. Construction works finally began in October 2010 and were expected to be completed before Euro 2012; however the deadline was not met and instead the airport began to operate in July 2012.
A new 5 km rail spur branching off from the existing Warsaw–Gdynia line will be built with an underground station at the airport, theoretically providing a 30-minute commute to Warsaw centre.
Although the first aircraft was meant to depart Modlin on 16 July 2012, the airport was officially inaugurated the day before, and the first passenger flight from Budapest arrived at the airport around 17:30. Low-cost-airlines Wizz Air and Ryanair started to use the airport as bases.
On 22 December 2012 it was announced that the runway at the airport would be closed to larger aircraft such as the Boeing 737 and Airbus A320 indefinitely for safety reasons. Ryanair confirmed on the day of the runway closure it would divert all aircraft to Warsaw-Chopin Airport until the runway was repaired. Wizz Air also confirmed that it would route its flights to Chopin Airport until Modlin re-opened.
The official re-opening took place over six months later on 4 July 2013 after construction works to fix the runway had been completed. On 17 July 2013, Wizz Air announced it would not return to Modlin despite its re-opening, but stay at Warsaw-Chopin Airport instead. Ryanair returned to Modlin on 30 September 2013.