With Federation in 1901, McGlinn was transferred to the new Commonwealth Postmaster-General's Department, working in Maitland as a telephone linesman.

McGlinn was acting commander of the 4th Brigade on Imbros from 17 October to 8 November, while Monash was in Egypt.

In this role he responsible for the processing of "casual reinforcements"; wounded men who had recovered and were being returned to their units.

For this work, he was appointed a Commander of the Order of the British Empire (CBE) in the 1919 New Year Honours.

On 11 November 1919, McGlinn was attached to AIF Headquarters as president of the courts-martial which tried Father O'Donnell,[1] the Australian Catholic Chaplain.

McGlinn returned to Australia in March 1920, and was placed on the unattached list as a brigadier general in July.

Returning to the PMG, McGlinn became deputy state engineer (lines) for New South Wales.

He died on 7 July 1946 and was buried at St Kilda Cemetery with full military honours.