Sir John Nelthorpe School accepts pupils from any Primary school and have welcomed pupils from a large number of local schools including the following:

Alkborough Primary
Barton St Peter's Church of England Primary
Bottesford Junior
Bowmandale Primary
Broughton Primary
Brigg Primary
East Halton Primary
Goxhill Primary
Hibaldstow Academy
John Harrison Church of England Primary
Kelsey Primary
Kirmington Church of England Primary
Kirton Lindsey Primary
Scawby Academy
Scotter Primary
South Ferriby Primary
St Barnabas Church of England Primary
St Mary's Catholic Primary
St Peter and St Paul Church of England Primary
The Grange Primary
Ulceby St Nicholas Church of England Primary
Waddingham County Primary
Winterton Junior
Worlaby Academy
Wrawby St Mary's Church of England Primary