Coming to office not long after the Xinhai Revolution had deposed the Qing dynasty, Aglen found himself heading a Chinese government department for a Republican administration whose influence often did not extend beyond Beijing.

[5] For his actions to continue the effective operation of the service and the maintenance of China's credit he was honoured by the President of the new 'Beiyang Government', Yuan Shikai, with the Second Class of the Order of the Precious Brilliant Golden Grain in April 1914.

Despite his success while in office, tensions between Aglen and the internationally recognised Beiyang Government increased as the power of the Kuomintang (KMT) spread north from their base in Guangdong Province.

The first Lady Aglen fell ill in early 1925 and Aglen took leave in order to accompany her with their newborn son George back to Britain in the hope that the climate would improve her health, leaving Hong Kong on board the Blue Funnel steamer SS Antenor on 7 April; however on 17 April, between Colombo and Singapore, she died at sea.

[16] His second son, Anthony John Aglen, was born in Beijing on 30 May 1911 and later rose to become a prominent British civil servant based in the Scotland Office and was awarded the Companion of the Order of the Bath (CB) in 1957 and a Fellowship of the Royal Society of Edinburgh in 1963.