Made a deacon in 1849, he was ordained as a priest in 1850 by Bishop Turton of Ely and worked as a curate in the Cambridge slums of Barnwell.
Scott planned a magnetic survey of the colony and reported that, despite the shortage of staff and equipment, 'the establishment is now complete in every respect'.
On 31 October 1862 Scott resigned as astronomer giving the reason as ill health, also reported as failing eyesight.
In the 1870s he preached frequently on the relation of religion to new scientific ideas but his public activities were not matched by any considerable energy at St Paul's.
However, he took eagerly to a country ministry at Gunning, Bungendore and Queanbeyan and later became a canon of St Saviour's Cathedral, Goulburn, and examining chaplain for Bishop Thomas.