On 26 February 1916, John Alexander Neilson applied for absolute exemption, stating: “Why I claim complete exemption is because I conscientiously object to take part in this or any war, because I believe that all life is sacred and war is nothing short than organised murder. My mission being to create love, not hate believing that all men are my brothers and so I am going to try in my way to establish the brotherhood of men here on Earth. I hope to live to see the day when any little differences between any Nation will be settled with reason and not with sword. So therefore I refuse to take part in any combatant or non-combatant service. I realise that such work as you would give me, would have one sole object, that being for the efficient conduct of war. I feel duty to stand by this convictions, whatever your decision, and I am prepared to demonstrate this by accepting the penalties inflicted.
He was not granted exemption and he appealed. On 12 May 1916, he was granted exemption from combatant service only. He was court-martialled in Hamilton on 22 June 1916 and sentenced to 112 days hard labour in Barlinnie Civil Prison where he served his sentence from 26 June 1916 to 23 September 1916. He was transferred to the Army Reserve Class W in November 1916.