McGregor served as the first chairman of the League's Management Committee. One of the committee's main jobs was handling issues of discipline, but committee members were not barred from involvement in decisions involving their own clubs. In fact, the first disciplinary meeting saw fines issued to three of the four clubs with representatives on the committee. McGregor was re-elected unopposed in 1891. Earlier he had spoken of his pleasure that "of the 132 matches in which the League clubs have taken part and in which about 300 players have taken the field, not a single fatal accident has to be recorded". A year later he oversaw the expansion of the Football League into two divisions when the rival Football Alliance was merged into the competition, but he relinquished his post later that year due to ill health, which caused him to miss meetings.