The former Pompey defender leaves his position in the club's academy to assist manager Andy Awford and fellow first-team coach Alan McLoughlin.
"I got a taste doing the job last season and Andy asked if I fancied making it a permanent arrangement," Hardyman told the club's official website.
"There was a lot to consider, but my heart was always telling me to say yes.
"Pompey are my home-town club so this is a fantastic opportunity for me and I get on really well with Awfs and Macca.
"Hopefully we can help put smiles on faces in the stands, just as we did at the end of last season."
Awford added: "I've worked with Paul for the last few years and we know each other inside out.
"I'm delighted to have both him and Macca alongside me in the first-team coaching set-up."