Arsenal scout Danny Karbassiyoon discovered Zelalem in the United States playing for Olney Rangers during a Dallas Cup match. After contacting his coaches, Zelalem was flown to London for summer training with the Arsenal youth academy; following the end of this camp, he was offered a permanent place in the Academy. Zelalem started out playing in Arsenal's under-16s squad, before graduating into the under-21s in April 2013. His début for the under-21 side came against Liverpool U21 that month, but was unable to prevent Arsenal slipping to a 3–2 defeat at Anfield; however, he drew praise for his performance. He made his second appearance for the side less than a week later in a 3–2 victory over Wolverhampton Wanderers U21, once again drawing praise for his performance.
In July 2013, Zelalem was included in Arsenal's 24-man squad for their Asia tour. Although regarded as a surprise inclusion, strong performances against an Indonesia Dream Team, the Vietnam national team and Japanese side Nagoya Grampus led to him being touted as a future star, and being compared favorably to Cesc Fàbregas.
Prior to making his one-time switch to the United States, Zelalem was eligible to represent Ethiopia internationally, due to his parents' nationality. In October 2013, Ethiopia's coach Sewnet Bishaw and Ethiopian foreign minister Tedros Adhanom stated that they hoped Zelalem would opt to play for Ethiopia, but Zelalem turned down the opportunity.
Before becoming an American citizen, Zelalem had previously played for Germany's youth teams. He played for Germany's under-15 and under-16 sides, making two appearances for the under-15s and eight appearances for the under-16s. In November 2013, Zelalem represented Germany at under-17 level in a friendly versus Spain. But in March 2014, he withdrew from the Germany under-17 national team for the Group 5 2014 UEFA European Under-17 Football Championship elite round fixtures, and again turned down the Germany under-18 national team for friendly matches versus France in March 2015, citing his desire to represent the United States instead.