Chan's first pastoral assignment was as assistant parish priest at the Church of St. Michael in Ipoh, then part of the Federated Malay States. He served in this role from 1939 to 1941, and again from 1944 to 1946 after the Japanese occupation of Malaya. Subsequently, he was transferred back to his hometown and served as parish priest of the Church of the Nativity of the Blessed Virgin Mary between 1946 and 1955. On the first day of every month, he organized a communal Rosary and offered a Mass to pray for all family members of parishioners who had died during the Japanese occupation of Singapore. He also founded the Catholic Young Men’s Association and the Children of Mary Movement during his time as parish priest. During his first two years as pastor, he resided at the St. Francis Xavier Seminary in Punggol. From December 1951 until October 1953, Chan's assistant at the Church of the Nativity was Gregory Yong, who would later go on to be Chan's successor as Bishop of Penang in 1968. One of Chan's noteworthy friendships was with Sultan Ibrahim of Johor. At the start of Chan's tenure as parish priest, the sultan gave Chan a marble statue of the Immaculate Conception of the Blessed Virgin Mary as a "token of friendship". The statue was blessed by Chan on 8 December 1946, the Solemnity of the Immaculate Conception, and it is still situated in the church courtyard as of 2020.
The earliest mention of Chan suffering from terminal cancer was in 1963. He was cared for by the French Sisters of the Foreign Mission. In spite of his ill health, he attended two out of the four sessions of the Second Vatican Council in 1962 and 1964, thus making him a Council Father. He made three trips to Hong Kong for specialist cancer treatment, the last one being in April 1967, and eventually he went blind in one eye as a result of the disease. He fell into a coma at his Macalister Road residence on the night of 20 October 1967, and died an hour and a half later, surrounded by four of his siblings who had arrived from Singapore and Ipoh earlier that same day. He was aged 54 and had been bedridden for the last three months of his life. He lay in state at his home before his funeral was held three days later on 23 October at the Cathedral of the Assumption. He was interred at the Western Road Cemetery in George Town. Chan was succeeded as Bishop of Penang by Gregory Yong on 1 July 1968. The cathedra that was first utilized by Chan at the Cathedral of the Assumption in 1955 is still in use, having been moved to Holy Spirit Cathedral when it was elevated to the status of cathedral in 2003.
Personal life
Chan had three brothers – Joseph, Anthony, and John – who resided in Singapore at the time of his death, and at least one sister, Teresa, who lived in Ipoh. He was a classical music aficionado, particularly for opera. During his years in the seminary, he played the flute for their orchestra, and frequently sang as a tenor for the choir at the Church of the Sacred Heart. This passion for music led to him being nicknamed "The Singing Bishop" during his time in Penang.