He is scheduled to hold talks with Azerbaijani President Ilham Aliyev and other top officials in an effort to reinvigorate EU-Baku ties.
Barroso previously visited Moldova and Georgia on his four-day trip.
In Chisinau and Tbilisi, Barroso reiterated the EU's support ahead of the two countries' expected signing of key Association Agreements with the bloc on June 27.
Talking to reporters in Tbilisi on June 12, Barroso said the EU is "ready to engage" in discussions with Russia if Moscow has concerns over Moldova and Georgia seeking closer ties with the bloc.
"Georgia has made a choice and we are here to support" that choice, Barroso said.