

Following his return to England, Pelham's knowledge of siege craft resulted in his employment by Portinari and Concio in improving the fortifications at Berwick against potential Franco-Scottish attack. The Privy Council was so impressed with his competency and judgement that he was promoted to Lieutenant-General of the Ordnance and spent the next few years strengthening the defenses of the realm. In the summer of 1579, Pelham was sent to Ireland to organize the defenses of the Pale against the rebellion of James FitzMaurice Fitzgerald, which threatened to spread from Munster. Knighted by Sir William Drury on 14 September of that year, he was elected lord Justice of Ireland on the latter's death on 3 October, and it was in this capacity that he presided over the well documented English military activity in the aftermath of FitzMaurice's rebellion and the subsequent suppression of the Earl of Desmond's uprising.
After returning to England in October 1580, in January of the following year, Pelham joined the Earl of Shrewsbury and Sir Henry Neville in the commission to escort Mary Queen of Scots from Sheffield Abbey to Leicestershire, and was promoted to Lieutenant-General of the Ordnance.
In July 1586, Pelham accompanied the Earl of Leicester to the Netherlands, where he was advanced to Marshal of the army, and took a bullet in the stomach defending his commander-in-chief while inspecting the defenses before Doesburg. He survived his injuries and was present at the siege of Zutphen in September 1586 when Sir Philip Sydney was mortally wounded, it is said, imitating Pelham's previous act of chivalry.