The 25-year-old was charged after an incident on Duke Street in Liverpool city centre at around 3.20am on December 22.
Appearing at Liverpool Magistrates' Court, Flanagan pleaded guilty to the charge of common assault against partner Rachael Wall.
The court heard that the footballer had been seen on CCTV assaulting the mother-of-two, with whom he has been in a relationship for 18 months.
Lionel Greig, mitigating, said that the victim had not provided a statement and there had been no previous instances of domestic violence in their relationship, adding that both parties were under the influence of alcohol at the time of the incident.
District Judge Wendy Lloyd said that she had been given a breakdown of the CCTV footage, which showed Flanagan assaulting his partner on "several occasions" and kicking her at one point.
The case was adjourned to January 17, when Flanagan will be sentenced.