Turkey’s airport industry has experienced substantial growth over the recent years, but few studies have analysed their operational efficiency. This paper uses Malmquist productivity index (classical and bootstrapping) to assess the operational performance of 21 Turkey airports during the period of 2009 through 2014. The findings indicated that the efficiency and productivity of the majority of the Turkish airports increased during the period under investigation. However, in the period of 2011–2012, a significant decline was observed in efficiency. The main reason of this stagnation is the significant increase in the physical capacity of the Turkish airports in 2011. The non-reflection of the increasing physical capacity to passenger and cargo traffic caused a decline in 2012. In spite of declining in the period of 2011–2012, efficiency values of Turkish airports have increased again since 2013. Moreover, decomposition of the Malmquist index showed that most Turkey airports experienced losses in efficiency; however, in terms of technology, they have progressed. Two significant factors (i.e. operating hours and percentage of international traffic) were identified by the Simar-Wilson double bootstrapping regression analysis as explaining variations in airport efficiency. •Airport performance evaluations are very important for the development of a country.•Turkey’s airport industry has experienced substantial growth over the recent years.•This study evaluates Turkish airports comparative efficiencies for 2009-2014 period.•Productivity of the majority of the Turkish airports increased during the related period.•In the period of 2011-2012, a significant decline was observed in efficiency.