[2] From 2002 until 2010, Ebner honed his skills in Admira's youth divisions before earning a promotion to the amateur team.

He made his debut in the Austrian Regionalliga East on 12 March 2010, against the amateurs of SV Mattersburg, contributing to a 3–0 away victory.

Ebner's debut in the Austrian Bundesliga transpired under the guidance of coach Dietmar Kühbauer on 24 March 2012, against eventual champions Red Bull Salzburg.

[4] Following an impressive stint of over 170 Bundesliga games with Admira, he moved to league rival Austria Wien for the 2018–19 season, where he signed a contract that ran until June 2021.

The game, which included Admira Wacker teammates such as Christoph Knasmüllner and Lukas Rath, ended in a 4–0 loss for the Austrians.