In 1912 he married Henrietta Hill, daughter of Thomas Scott of Hannaville, Greenisland, County Antrim.
On Luke's unexpected death in 1897, John Hayden was adopted as the Parnellite candidate to succeed him at South Roscommon.
In spite of his role as a land campaigner, in the early 1900s Hayden was himself the target for hostile agitation headed by Laurence Ginnell, who saw him as symbolising the Irish Party's hypocritical tolerance of ‘grazing’, the operation of large tracts of land for cattle-rearing rather than as smaller holdings for poorer farmers.
He was consulted by Redmond before he made his historic statement in the British House of Commons in August 1914 committing Irish Volunteer support for Britain and her Allies and in the First World War.
After his Parliamentary defeat, Hayden continued to take an active part in the editorship of the Westmeath Examiner until a fortnight before his death.