Samuel Rutherford was born around the turn of the seventeenth century, at about the same time as both Charles I and Oliver Cromwell. Although the evidence for his early life is very fragmentary indeed, we know that he was born and grew up in the south-east of Scotland, almost certainly in the town of Nisbet in the parish of Crailing, not far from the English border. In his only personal reference to the first twenty years of his life – in a letter to the minister of Oxnam, the neighbouring parish to Crailing – Rutherford expressed his spiritual concern for the area, ‘that place to which I owe my first breathing’. Although it has one large hill, the parish is an area of rich and fertile arable land, and the lowest, warmest and most attractive part of the basin of the river Teviot, which wends its way eastwards between the small towns of Nisbet and Crailing.

Rutherford's first biographer, Robert McWard, wrote that he was ‘a gentleman by extraction’, and Robert Wodrow claimed that he was ‘the son of an heretor [landowner]’. Others have suggested that his father was a farmer or a miller, possibly Andrew or William Rutherford, both of whom were involved in a feud in the parish in 1596. Although this cannot be substantiated, it is clear that Rutherford's family was neither particularly poor nor especially distinguished.