Andrew Johnstone was born in Preston, Lancashire in 1967 and began his education at a special school for the partially sighted. He took his first lessons in organ-playing and harmony from the noted blind teacher John Robinson, and spent three years as organ scholar of Worcester College, Oxford, where he studied with Robert Sherlaw Johnson, Thomas Trotter and David Sanger. He subsequently held the organ scholarship at Chichester Cathedral before moving to Dublin in 1989 as assistant organist at St. Patrick's Cathedral.
A first-class honours graduate of Oxford, he holds the Fellowship Diploma of The Royal College of Organists for which he was awarded the Limpus Prize for the highest marks in organ-playing.