"Overall, at regional level, the analyzed quarter detections of Syrian migrants increased significantly (+260 percent) compared to the previous three months," Frontex said in its second-quarter analysis.
It added that the Serbian-Macedonian border accounted for 88 percent of detections at border crossing points.
The agency said the roughly 52,200 non-residents who were seen illegally crossing the Western Balkan borders represented a 219-percent increase compared to January-March this year.
The Western Balkans are made up of Croatia, Serbia, Bosnia and Herzegovina, Montenegro, Kosovo, Macedonia and Albania.
The region serves as one of transit points for people fleeing crises-ridden home countries in the Middle East and North Africa in an attempt to gain asylum in EU member states.
The number of migrants reaching EU borders has seen an unprecedented spike this summer. Frontex noted a threefold increase of illegal crossings into the EU's external borders as of July compared to last year.