Unfortunately
Fanningstown does not surface in the historical record until the late
sixteenth century. By this time the English, conscious that their
power was slipping from them in Ireland, were determined to reassert
themselves. One strategy was the appointing of a new breed of ambitious
administrator such as Sir Warham St Leger, who became Lord Justice
in 1569.With
the granting of the tithes of Ballyfenninge to him in 1567 Fanningstown
had fallen into the English orbit. This was important for the Fitzgerald
earldom of Desmond, which controlled large swathes of Munster, including
many of the old Norman fortresses, were opposing English efforts at
centralisation.

In 1569
this resolved itself into rebellion, which lasted until James Fitzmaurice
Fitzgerald submitted in 1573 before going into exile. When he returned
with fresh soldiers in 1579 a new phase in the rebellion started.
It was to Fanningstown that Sir William Pelham, now Lord Justice,
camped with a large force, summoned the Earl of Desmond to meet him.
When
Desmond failed to make the rendezvous Pelham charged him with treason
and instituted a scorched earth policy which reduced Munster to a
famine that lived long in the folk memory. Gradually Pelham captured
the castles that had supported Desmond; Limerick, Croom, Kilmallock,
Lough Gur, and finally Askeaton.
The Rebellion
was finally crushed in 1583 with the killing of the Earl of Desmond.
Fanningstown was granted to the succeeding Lord Justice, Sir H. Wallop,
in 1592.