Younan has been actively engaged in the Middle East Council of Churches, in various positions since 1985 including as the president of its Evangelical Family until 2018. Younan served as president of the Fellowship of the Middle East Evangelical Churches (FMEEC) in 2004–2010, which during his presidency unanimously voted if favor of the ordination of women as pastors. Younan is also a founding member of the Ecumenical Accompaniment Programme in Palestine and Israel (EAPPI), serving as the chair of Local Reference Group since 2002.