Penney was arrested in the early hours of Sunday morning on Southend seafront, just hours after the Blues won a dramatic Wembley play-off final to secure promotion to League One.
The 50-year-old, who has been assistant to manager Phil Brown since 2013, took his place on the team’s open-top bus parade on Monday wearing dark glasses and with a cut on his forehead.
The former Doncaster Rovers, Darlington, Oldham and Bristol Rovers boss Penney, will appear at Castleford’s magistrates on 8 June.
Southend, who sealed promotion with a 7-6 penalty shout-out win over Wycombe Wanderers, have yet to comment on the incident.
A 24-year-old woman from Yorkshire was cautioned for assault.