Mohamad began his career at Safa Sporting Club, signing to the first-team from the youth team. He got promoted to the first team in 1999 and played for 3 years, making 25 league appearances and scoring 3 times.

On 16 August 1999, Mohamed debuted for Lebanon in the 1999 Pan Arab Games. On 25 June 2000, Mohamad scored a free kick, his first international goal, in a 3–1 home victory against Kuwait.

In 2000, aged 20, Mohamad was selected to represent Lebanon at the 2000 Asian Cup. This opportunity of playing in a major tournament at a young age gave him a big chance to broaden his career. On 12 October, he played a full 90 minutes in Lebanon’s opening 4–0 loss against Iran. On 15 October, he was substituted onto the field in the 89th minute for Abbas Chahrour in a 2–2 draw against Iraq. However, he would not take part in Lebanon’s 1–1 draw with Thailand on 18 October.

In 2002, he transferred to Olympic Beirut, a club that was founded in 2000. Mohamed went on to win the Lebanese Premier League and Lebanese FA Cup titles in 2003.

Mohamad scored in a friendly match against Bahrain on 19 September 2003.

Mohamad joined Freiburg from Olympic Beirut] in 2004 at the recommendation of his international teammate, Roda Antar. He scored his first goals, a brace, in a 3–3 draw against Greuther Fürth on 22 September 2006. Although Freiburg were relegated to the 2. Bundesliga, Mohamad remained there until his transfer to 1. FC Köln in 2007 along with Roda Antar.

Mohamad signed for Köln on 17 July 2007. They were promoted to the German first division for the 2008–09 season after Youssef and his team-mate Roda Antar made a great season.

During 2007, Mohamad reportedly had a disagreement with Lebanon’s assistant coach Adnan Meckdache where he had intensely criticized the Lebanese Football Federation and the national team coach. He was suspended by the Football Federation and would be allowed to return on the condition that he would apologize to the Lebanese F.A. and its national team coach for the critical stance.

In January 2010, Köln coach Zvonimir Soldo announced that Mohamad would be the captain of the club.

On 19 August 2011, the official website of Al-Ahli announced that they had come to an agreement with 1. FC Köln for the transfer of Mohamad to the UAE League. Mohamad had reportedly signed a two-year contract after successfully passing a medical. It was reported that Köln would not allow Mohamad to leave until they could find a replacement for him, and the club board said that it was an honour to have the Lebanese defender.

After retiring from football, in 2016 Youssef Mohamed took the role of technical advisor for the Lebanon national team.