Croatian Transport Minister Oleg Butkovic was aboard and said the flights connected the two friendly countries and provided a better connection with Europe and the rest of the world.
Croatia Airlines will fly between Zagreb and Mostar throughout the year on Thursdays and Sundays, and between Mostar and Zagreb on Fridays and Mondays.
"Connecting Mostar and Zagreb represents the connecting of two friendly countries and good neighbours, Croatia and BiH," Butkovic told reporters in Mostar, adding that the flights were also expected to help the economic development of the Mostar area.
"Connecting Zagreb and Mostar in one hour makes it possible to connect not just the two cities but also to connect them with Europe and the world as many flights take off from (Zagreb's) Franjo Tudjman Airport. This way we are making it possible for a large number of tourists to arrive here in Mostar, Medjugorje, this beautiful part of BiH," said Butkovic.
As of mid-May, Mostar will have direct Eurowings flights to and from Stuttgart, Germany on Wednesdays and Saturdays.