He was posted to his unit on the Dardanelles, on 23rd August 1915, and five days later on 28th August, was reported with a shrapnel wound to his left shoulder, and was briefly reported missing. He was admitted from Anzac Cove to a Hospital Ship, HS Devanagh, on 29th August for transport to Malta. He arrived there on 4th September, and was admitted to the Cottonera Military Hospital, where he was reported dangerously ill with a gun shot wound to his arm. By1 3th November he was out of danger and was transferred to the Hospital Ship Maheno, for return to New Zealand on 21st November 1915.

A year later John Patterson sailed on HS Marama, returning to England for further medical treatment. He was admitted to No 1 NZG Hospital Brockenhurst, on 31/12/1916, to have his left arm amputated. He was then transferred to Hornchurch on 31th January 1917, from Hornchurch to Rockhampton on 26th February 1917 where he was fitted with an artificial limb. He then spent a week in Walton-on-Thames hospital before transferring to the NZ Discharge Depot at Torquay on 13th June 1917. On the 10th of July Headquarters London reports that he had forfeited 1 weeks pay and was CB (Confined to Barracks) for 7 days, as punishment for being absent. Finally he embarked from Plymouth on 26th July aboard the SS Rimutaka, bound for New Zealand.

On 18th November 1917, a month following his return to New Zealand Trooper John Patterson was discharged from the NZEF, no longer fit for active service on account of wounds received while on active service.