The paper presents the application of a non-parametric data envelopment analysis (DEA) technique for measuring the macroeconomic performance of the Balkan countries. In this context, for the period of 2006–2018, a dynamic DEA Window model was applied based on selected macroeconomic indicators as input and output variables. For a more comprehensive and objective analysis, the DEA Window analysis is complemented by a Malmquist productivity index that provides a more complete picture of the observed entities' performance and shows a trend of change from period to period. The results showed that in the observed period, Albania and to a large extent Montenegro, especially after the end of the global financial crisis, had the highest average efficiency, that is, they used the available resources effectively to increase the GDP growth rates. The EU Member States, Greece and Croatia, in particular, achieved the highest growth in overall productivity over the observed period, and this growth was largely due to a change in technical efficiency.