Stainer’s output was so great that space does not permit the provision of a full list. The fullest inventory can be found as an appendix to Peter Charlton’s biography of Stainer: John Stainer and the Musical Life of Victorian Britain. Newton Abbot, 1984. The following list is based upon one published in the Musical Times (1 May 1901) as part of an obituary notice.

• Gideon (his exercise for the degree of Doctor of Music)

• The Daughter of Jairus, Worcester Festival, 1878

• St Mary Magdalen, Gloucester Festival, 1887

• Crucifixion, first performed at St. Marylebone Church, February 24, 1887.

158 hymn tunes, collected in one volume, 1900.

The following are generally regarded as the most outstanding:

• Gracious Spirit, Holy Ghost. (Tune: Charity).

• The Saints of God! (Rest).

• There’s a friend for little children. (In Memoriam).

• Antiphons, The Seven Greater.
• And all the people saw the thunderings. Composed for the London Church Choir Association Festival, St. Paul’s Cathedral, November 8, 1883.
• And Jacob was left alone.
• Awake, awake, put on thy strength, O Zion.
• Behold, God is my Helper.
• Behold, two blind men sitting by the wayside.
• Blessed is the man that endureth temptation.
• Deliver me, O Lord, from mine enemies.
• Drop down, ye heavens, from above.
• For a small moment have I forsaken Thee.
• Grieve not the Holy Spirit of God.
• Honour the Lord with thy substance.
• Hosanna in the Highest.
• I am Alpha and Omega.
• I desired wisdom openly in my prayer.
• I saw the Lord.
• It came upon the midnight clear.
• Lead, kindly Light.
• Leave us not, neither forsake us.
• Let every soul be subject unto the higher powers. (Composed for the jubilee of Queen Victoria, 1887).
• Let not thine hand be stretched out to receive.
• Let the peace of God rule in your hearts.
• Lord, Thou art God.
• Lo! summer comes again.
• Mercy and truth are met together.
• bountiful Jesu, O sweet Saviour.
• O clap your hands.
• Saving Victim, slain for us.
• Zion that bringest good tidings.
• Sing a song of praise.
• The hallowed day hath shined upon us.
• The Lord is in His holy temple.
• The morning stars sang together.
• The righteous live for evermore.
• The Story of the Cross.
• There was a marriage in Cana of Galilee.
• They have taken away my Lord.
• They were lovely and pleasant in their lives.
• Thou, Lord, in the beginning.
• Thus speaketh the Lord of Hosts.
• What are these that are arrayed in white robes?
• Ye shall dwell in the land.

• Several complete sets of church services.

• Several settings for Holy Communion (in various keys).

• Carols (various, including a collection edited in collaboration with the Rev. H. R. Bramnley).

• Twelve sacred songs for children (originally published as Holy gladness and illustrated).

• Editor of St. Paul's Cathedral Chant Book.

• One of the editors of the Cathedral Psalter and of the Cathedral Prayer Book.

• The Seven-fold Amen.

• Madrigals, including the Triumph of Victoria and Flora's Queen (the words by his son, J. F. R. Stainer).

• Part-songs.

• A Book of Seven Songs

• Six Italian Songs

• Various single songs.

• Twelve pieces (in two books).

• Jubilant March.

Stainer’s most important works are the following:

• A Theory of Harmony. London: Rivington, 1871.

• A Dictionary of Musical Terms. London: Novello, 1876.

• The Organ. London: Novello, 1877.

• Harmony. London: Novello, 1878.

• Composition. London: Novello, 1877.

• Choral Society Vocalisation. London: Novello, 1877.

• Dufay and His Contemporaries. London: Novello, 1896.

• Early Bodleian Music. London: Novello, 1901.