The tie will likely be played at Priestfield on Saturday November 3, as it is unlikely to be considered for live TV coverage.
Gillingham have enjoyed a great start to the season under Martin Allen, and top League Two with 32 points from 13 games.
They are unbeaten in the league, with their only defeats coming in cup competitions.
They bowed out of the Johnstone's Paint Trophy with a 3-2 loss to Crawley Town, while their Capital One Cup campaign was ended in the second round with a 2-0 home loss to Middlesbrough. They had claimed the scalp of Bristol City with a 2-1 win at Ashton Gate in the first round of that competition.
Draw in full:
Kidderminster Harriers v Oldham Athletic
Hayes & Yeading / Boreham Wood v Brentford
Chelmsford City / East Thurrock United v Colchester
Metropolitan Police v Crawley Town
Luton Town v AFC Telford / Nuneaton Town
Portsmouth v Notts County
Bishop's Stortford v Hastings United
Fleetwood Town v Bromley
Forest Green Rovers / Dartford v Port Vale
Torquay United v Hyde / Harrogate Town
AFC Bournemouth v Dagenham & Redbridge
Morecambe v Rochdale
Swindon Town v Macclesfield Town
Cambridge City v MK Dons
Cheltenham Town v Yate Town / Newport County
Dorchester Town v Plymouth Argyle
Coventry City v Arlesey Town
York City v AFC Wimbledon
Bury v Exeter City
Chesterfield v Hartlepool United
Doncaster Rovers v Bradford Park Avenue
Gillingham v Scunthorpe
Aldershot v Hendon
Lincoln / FC Halifax v Walsall
Wrexham v Alfreton Town
Southend United v Stockport County
Crewe Alexandra v Wycombe Wanderers
Bristol Rovers v Sheffield United
Hereford United v Shrewsbury Town
Mansfield Town v Slough Town / Gosport Borough
Barnet v Oxford United
Rotherham United v Stevenage
AFC Fylde / Ilkeston v Accrington Stanley
Gloucester City v Leyton Orient
Burton Albion v Altrincham
Guiseley v Barrow
Northampton Town v Bradford City
Preston v Yeovil Town
Braintree Town v Tranmere Rovers
Carlisle United v Ebbsfleet United