Youssef began his coaching career as an assistant coach at Al–Ahly's first team in June 2009 until April 2013. On 7 May 2013, Youssef was promoted as head coach. He led
Al-Ahly to win the
2013 CAF Champions League, and reached the
2013 FIFA Club World Cup. in Morocco. On 1 May 2014, he resigned from Al-Ahly. On 23 July 2014, he was appointed as manager of
Iraqi Premier League champions
Al Shorta SC. Despite winning 11 and drawing 4 of the 15 league games he took charge of and was leading their group in the
AFC Cup, he was sacked in May 2015. In July 2015, he became head coach of
Smouha in the Egyptian premier league, playing also with the Alexandrian club in the
CAF champions league. In July 2016, he returned to
Iraqi Premier League Al Shorta SC as head coach. In July 2017, he became head coach of
Petrojet in the
Egyptian premier league. In June 2018, Youssef returned to Al-Ahly as an assistant coach and sports director till the end of his contract on 31 August 2019. On 19 October 2020, he was appointed as the head coach of the newly promoted
National Bank of Egypt. In November 2022, he was appointed as head coach of
Tala'ea El Gaish, following a tenure as technical director at
Future in 2021. On 4 February 2024, he was named as caretaker coach of the
Egyptian national team, following the dismissal of
Rui Vitória. Two days later,
Hossam Hassan became the head coach of Egypt, and Youssef refused to take an administrative manager role. ==Managerial statistics==