In 1867 he was articled to George Fosbery Lyster, engineer in chief to the Mersey Docks and Harbour Board, with whom he remained until 1870.
He was next employed as resident engineer to the Persian railways of Baron de Reuter and afterwards in supervising the construction of docks at Leith and at Boston, Lincolnshire.
[5] Meanwhile, Allen was interested in archaeology; and he spent the rest of his life on it, and particularly on the study of prehistoric antiquities and of pre-Norman art in Great Britain.
His earliest contribution was to Archæologia Cambrensis ("A description of some cairns on Barry Island"), appearing in April 1873; he joined the Cambrian Archaeological Association in 1875, was elected a member of the general committee in 1877, became one of two editors of its Journal in 1889, and was sole editor from 1892 until his death.
Having begun with the antiquities of Wales, Allen from 1880 gave attention to those of Scotland also; in 1883 he was elected fellow of the Scottish Society of Antiquaries, and in 1885 was Rhind Lecturer in archaeology in the University of Edinburgh.