The former Premier League footballer, who spent most of his career at Manchester City and won one cap for England, will appear in court later this month.
Cheshire Police said the charges concerned messages sent by the 41-year-old between 1 and 18 January.
In a statement, a force spokesman said: ‘A man from Widnes has been summoned to court to face charges of malicious communications.
‘Following an investigation by Cheshire Police, the Crown Prosecution Service has since authorised the charges for Joseph Barton.’
Barton has repeatedly criticised Aluko, who made 102 caps for England between 2004 and 2016 and has since moved into punditry.
Responding to the charge on X, he said: ‘I’m up next month for ‘malicious communications’ charge at Warrington Mag for Eni Aluko tweets.
‘Crazy times we’re living in. Haven’t the police got enough on their hands?
‘British system is becoming a Banana Republic. Lawfare used against its own citizens for having a dissenting voice.’
Back in Feburary, Aluko accused Barton of subjecting her to ‘one of the worst cases of social media abuse I’ve ever experienced’.
‘How is she even talking about men’s football? She can’t even kick a ball properly,’ Barton posted on X in January.
‘Your coverage of the game EFC last night, took it to a new low. Eni Aluko and Lucy Ward, the Fred and Rose West of football commentary.’
Barton then wrote that Aluko was ‘clearly in the Joseph Stalin category’ for ‘murdering hundreds of thousands of fans’ ears’.
Discussing the abuse she has received, Aluko said in February: ‘It’s really important to say that online abuse has a direct impact on your safety and how you feel and how safe you feel in real life.
‘I’ve felt under threat this week. I’ve felt like something is going to happen to me.
‘And I don’t say that for anyone to feel sorry for me – I say that for people to understand the reality and the impact that hate speech has, the impact that racism has, the impact that sexism has, the impact that misogyny has on all of us females in the game, in sports broadcasting.
‘That’s the real impact – and it’s not an isolated incident, this is now showing up as a culture in the game, from certain fan bases and certain people.
‘They’re creating a culture where people don’t want to go to work, people don’t want to leave their house, people feel under threat. Obviously there’s a big impact on mental health as well.’
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