On 10 August 2007, the trustees of
St Patrick's College, Maynooth, announced his appointment as president in succession to
Dermot Farrell. In March 2011, Connolly denied rumours that Maynooth Seminary may be closing. "Media reports today about the possible closure of the seminary are without foundation. The media outlet leading with this incorrect story was sent a reply from us yesterday and its absence from the published copy is disappointing and damaging." A year later, when the
Summary of the finding of the Apostolic Visitation in Ireland was published, there was no reference to seminary closures but there were recommendations to improve the quality of seminary formation. In his capacity as rector of the national seminary, Connolly spoke on the dearth of vocations to the diocesan priesthood in Ireland. He was reappointed for a second term as president on 29 May 2012 at the summer meeting of the college trustees. In June 2016, it was announced that Connolly was taking a sabbatical year for the final year of his statutory ten-year term as president which concluded on 31 August 2017, nonetheless, it was an announcement that created some reporting that needed clarification. It was noted that the move was in accordance with the new sabbatical provisions of the Pontifical University, adopted some years earlier to reflect standard practice in the third level sector. Several months later advertisements were placed seeking a new college president, to assume office on 1 September 2017. He was succeeded in the post by Fr Michael Mullaney. Throughout his time as president, Connolly sought to raise the international profile of the Pontifical University at Maynooth and served as one of two board members for the Continent of Europe on IFCU the umbrella body for rectors of Catholic Universities worldwide. ==Post-Maynooth Ministry==