Although he intended to make the ministry his life’s work, Drury first entered upon a period of teaching at Pomfret School, combining with it theological studies which he pursued at the Berkeley Divinity School. In June 1905 he was ordained deacon. Soon afterwards he went to the Philippines as assistant to his friend Bishop Brent. During his two years in the Philippines he organized and conducted the Baguio School for native boys and did missionary work among the Igorotes. After his return to Boston he was ordained priest, and in 1908 he became rector of Calvary Church in Providence. Later that year he accepted an appointment as vicar of St. Stephen’s Church in Boston.

Dr. Ferguson had for some time been seeking a candidate to succeed him as Rector. On Sunday, December 8, 1908, Drury preached in the Chapel of St. Paul’s School. That evening he addressed the Missionary Society and described his school in the Philippines and his work there. On the following morning, Dr. Ferguson asked him to come to St. Paul’s the next year as a master and intimated to him that he would be made vice-rector with the right to succession as Rector. Thus from December 9, 1908, Samuel Drury was destined to be Dr. Ferguson’s successor as Rector of St. Paul’s School.