Joly was elected a Fellow of the Royal Society of London in 1892, was awarded the Boyle Medal of the Royal Dublin Society in 1911, the Royal Medal of the Royal Society of London in 1910, and the Murchison Medal of the Geological Society of London in 1923. He was also conferred honorary degrees by the National University of Ireland, the University of Cambridge, and the University of Michigan. After his death, his friends subscribed the sum of £1,700 to set up a memorial fund which is still used to promote the annual Joly Memorial Lectures at the University of Dublin, which were inaugurated by Sir Ernest Rutherford in 1935. He is also remembered by the Joly Geological Society, a student geological association established in 1960.