Henniker-Hughan was the second son of Sir Brydges Henniker Bt. (of Newton Hall in Essex) and Louisa Hughan of Airds House, Parton, Galloway. As he was the second son, and not expected to inherit, he was bequeathed the Hughan family estates in Galloway by his maternal grandfather (Thomas Hughan). He inherited following the death of his aunt in 1896, at which point he took the second surname Hughan. Following the sudden and unexpected death of his brother, Colonel Sir Frederick Henniker, in late 1908 he succeeded to the Henniker Baronetcy as well (as the sixth Baronet), but continued to live at Airds in Galloway.