Batten attended Westminster School and Trinity College, Cambridge, and graduated in medicine in 1891 from St Bartholomew's Hospital Medical College in London. He worked as a pathologist at the Hospital for Sick Children and as a physician at the National Hospital. He obtained his doctorate in 1895, became a fellow of the Royal College of Physicians in 1901, and was elected dean in 1908. Batten disease was named after him after he first described it in 1903.
- E. Chaves-Carballo (1979). "Eponym: Frederick E. Batten: father of pediatric neurology". Southern Medical Journal. 71 (11): 1428–1429. doi:10.1097/00007611-197811000-00033. PMID 362542.
- "Batten, Frederick Eustace (BTN884FE)". A Cambridge Alumni Database. University of Cambridge.
- Sara Mole; Ruth Williams; Hans Goebel (10 March 2011). The Neuronal Ceroid Lipofuscinoses (Batten Disease). Oxford University Press. pp. 10–. ISBN 978-0-19-959001-8.