He was completing his master's degree at Queens University Belfast when he followed the call of John Redmond to join the war effort and ensure Irish Independence.

After the start of the Civil War, he was put in command of troops charged with taking posts held by the anti-Treaty IRA in Limerick.

[5] His troops successfully dislodged the anti-Treaty IRA from positions around Killmallock in Limerick but Murphy was criticised for his tendency to 'dig in' and resort to trench warfare rather than rapid offensive action.

In the early stages of the guerrilla war, he organised large-scale 'sweeps' to break up the republican concentrations in west Cork and east Kerry.

[7] Murphy exercised overall command in the county but day-to-day operations were largely run by Brigadier Paddy Daly, of the Dublin Guard.

[8] In October, in response to continuing guerrilla attacks on his troops, Murphy ordered a curfew to be put into place in Tralee from 10:30 until 5:39 every night.

[9] In December, Murphy wrote to Mulcahy that the "Irregular [Anti-Treaty] organisation here is well nigh broken up", and suggested the end of the war in the county was in sight.

[10] On 20 December, Murphy sentenced four captured republican fighters to death under the Public Safety Act for possession of arms and ammunition.

Humphrey Murphy, the local IRA Brigade commander, threatened to shoot eight named government supporters in reprisal if the men were executed.

Murphy later voiced the opinion that Daly had been a bad choice, given his implication in the Ballyseedy massacre and other events of March 1923, in which up to 30 anti-Treaty prisoners were killed in the county.