In 1760 his father moved to his ancestral house at Holme, in the township of Cliviger, Lancashire, and the boy was in November 1766 placed under the care of the Rev.
William Sheepshanks of Grassington in Craven, he was admitted to St John's College, Cambridge, and went into residence in October 1775.
He married, 13 January 1783, Lucy, daughter of Thomas Thoresby of Leeds, and left several children, of whom one, Robert Nowell Whitaker, also became vicar of Whalley.
His library was sold at Sotheby's in 1823, and his coins and antiquities, with the exception of his Roman altars and inscriptions, which he bequeathed to St John's College, Cambridge, were dispersed in 1824.
His published works were: Whitaker re-edited Ralph Thoresby's Ducatus Leodiensis (2nd edition, with notes and additions, 1816).
He published ten occasional sermons and a political speech, and wrote dozens of articles for the Quarterly Review between 1809 and 1818.