Batten attended Westminster School and Trinity College, Cambridge, and graduated in medicine in 1891 from St Bartholomew's Hospital 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, Frederick Eustace (BTN884FE)". A Cambridge Alumni Database. University of Cambridge.
- E. Chaves-Carballo (November 1979). "Eponym: Frederick E. Batten: father of pediatric neurology". Southern Medical Journal 71 (11): 1428–1429. PMID 362542.
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