McFall left school with no qualifications at the age of 15. He later returned to education, gaining a BSc in Chemistry from Paisley College of Technology. Following this, while working as a teacher of maths and chemistry, he gained a BA in Education and Philosophy from the Open University.
In May 2008 in the abortion amendments to the Human Fertilisation and Embryology Bill (now Act), John McFall voted for the abortion time limit to be lowered to 12 weeks against scientific and medical consensus which is currently 24 weeks. After four separate parliamentary votes on varying time limits, the majority of MPs voted to keep the abortion time limit at 24 weeks, in keeping with scientific and medical consensus, hence no abortion amendments were added to the bill.