He studied at Winwick grammar school, of which he was appointed a master in his fifteenth year, and left it in 1612 to become master of a newly established school at Toxteth Park, Liverpool. After a few months at Brasenose College, Oxford, he began in November 1618 to preach at Toxteth, and was ordained there, possibly only as deacon, early in 1619.
Between August and November 1633 he was suspended for nonconformity in matters of ceremony; and in 1634 was again suspended by the visitors of Richard Neile, archbishop of York, who, hearing that he had never worn a surplice during the fifteen years of his ministry, refused to reinstate him and said that "it had been better for him that he had begotten seven bastards".
He had a great reputation as a preacher in and about Liverpool; but, advised by letters of John Cotton and Thomas Hooker, he was persuaded to join the company of pilgrims in May 1635 and embarked at Bristol for New England.
On 3 June 1635, Richard, wife Katherine, and children Samuel, Timothy, Nathaniel, and Joseph, all set sail for the New World aboard the ship James. As they approached New England, a hurricane struck and they were forced to ride it out just off the coast of modern-day Hampton, New Hampshire. According to the ship's log and the journal of Increase Mather, the following was recorded;
At this moment,... their lives were given up for lost; but then, in an instant of time, God turned the wind about, which carried them from the rocks of death before their eyes. ...her sails rent in sunder, and split in pieces, as if they had been rotten ragges...
They tried to stand down during the storm just outside the Isles of Shoals, but lost all three anchors, as no canvas or rope would hold, but on 13 August 1635, torn to pieces, and with not one death, all one hundred plus passengers of the James managed to make it to Boston Harbor.
As a famous preacher "he was desired at Plimouth, Dorchester, and Roxbury". He went to Dorchester, where the Church had been greatly depleted by migrations to Windsor, Connecticut; and where, after a delay of several months, in August 1636 there was constituted by the consent of magistrates and clergy a church of which he was "teacher" until his death in Dorchester on 22 April 1669. He was buried in the Dorchester North Burying Ground.
He was a leader of New England Congregationalism, whose policy he defended and described in the tract Church Government and Church Covenant Discussed, in an Answer of the Elders of the Severall Churches of New England to Two and Thirty Questions (written 1639; printed 1643), an answer for the ministers of the colony to 32 questions relating to church government that were propounded by the general court in 1639. He drew up the Cambridge Platform of Discipline, an ecclesiastical constitution in seventeen chapters, adopted (with the omission of Mather's paragraph favouring the "Half-Way Covenant", of which he strongly approved) by the general synod in August 1646. His Reply to Mr Rutherford (1647) is a polemic against the Presbyterianism to which the English Congregationalists were then tending.
With Thomas Welde, Thomas Mayhew and John Eliot he wrote the "Bay Psalm Book", or, more accurately, The Whole Booke of Psalmes Faithfully Translated into English Metre (1640), probably the first book printed in the English colonies. He was the author of Treatise on Justification (1652).
Mather married in 1624 Katherine Hoult or Holt (died 1655), and secondly in 1656 Sarah Hankredge (died 1676), the widow of John Cotton. Of six sons, all by his first wife, four were ministers:
- Samuel (1626–1671), the first fellow of Harvard College who was a graduate, chaplain of Magdalen College, Oxford, in 1650–1653, and pastor (1656–1671, excepting suspension in 1660–1662) of Church of St. Nicholas Within Dublin; 
- Nathaniel (1630–1697), who graduated at Harvard in 1647, was vicar of Barnstaple, Devon, in 1656–1662, pastor of the English Church in Rotterdam, his brother's successor in Dublin in 1671–1688, and then until his death pastor of a church in London;
- Eleazar (1637–1669), who graduated at Harvard in 1656 and after preaching in Northampton, Massachusetts, for three years, became in 1661 pastor of the church there;
- Increase (1639–1723) was a Puritan minister and a major figure in the early history of the Massachusetts Bay Colony and Province of Massachusetts Bay (now the Commonwealth of Massachusetts).
Horace E. Mather, in his "Lineage of Richard Mather", (Hartford, Connecticut, 1890), gives a list of 80 clergymen descended from Richard Mather, of whom 29 bore the name Mather and 51 other names, the most common being Storrs and Schauffler.
- Greaves, Richard L (1998), Dublin's Merchant-Quaker: Anthony Sharp and the Community of Friends, 1643 – 1707, Stanford University Press, p. 4, ISBN 9780804734523
- This article incorporates text from a publication now in the public domain: Webster, Richard (1911). "Mather, Richard". In Chisholm, Hugh. Encyclopædia Britannica 18 (11th ed.). Cambridge University Press. pp. 885–886.
- This article incorporates text from a publication now in the public domain: Frederic Gregory Mather (1900). "Mather, Richard". In Wilson, James Grant; Fiske, John. Appletons' Cyclopædia of American Biography. New York: D. Appleton.
- Clapp, Ebenezer (1859), History of the Town of Dorchester, Massachusetts, Boston
- Gordon, Alexander (1885–1900). "Mather, Richard". Dictionary of National Biography. London: Smith, Elder & Co. pp. 29–30.
- Mather, Richard (1850), Journal of Richard Mather 1635 His Life and Death 1670.