Barker has worked alongside Karl Robinson at League One Charlton since December 2016 but was approached by Rotherham last week.
The 41-year-old had three spells with the Millers as a player, scoring 13 goals in 153 league games.
Rotherham will join Charlton in League One next season following their relegation from the Championship.
Barker and Warne were team-mates when the Millers won promotion to the second tier 2000-01.

Giving evidence, the anonymous 72-year-old said Brother Lawrence Murphy took him in to his bedroom twice, forcing him to perform sex acts.
If I had told anyone, I would have been belted or got the strap, he said.
Castledare orphanage near Perth, run by the Christian Brothers order, was like "a legal paedophile ring", he said.
The witness told the inquiry: "If someone did it in the public eye, he'd go to court, he'd get sentenced and he'd serve time.
"If he'd got a habit on, if you're a Christian Brother then it seemed to be a free-for-all.
"We knew what would happen if you told somebody, especially in authority, they would say 'this doesn't happen here.'"
The abuse scandal of the British children sent abroad
'Name the villains', abuse inquiry told
He went on to claim that Brother Murphy was later "transferred from place to place" to effectively hide him.
He said his time at the orphanage still haunted him and was "probably something I will never forget".
He had bottled it up for nearly 30 years and had only chosen to speak out when he found out about the inquiry, he added.
Life for the orphans involved hard physical labour including pulling down trees, clearing land, digging out a swimming pool and building a handball court by chipping bricks.
"You had to chip X amount of bricks before you can knock off, before you had something to eat," he told the inquiry, which is looking into abuse in England and Wales.
The boys wore only a grey shirt and shorts, no matter what the weather, he said.
There were no underpants and shoes were only worn when somebody important visited, otherwise feet were bare, he added.
Brothers would be fully clothed with shoes and gloves while the boys shivered in the cold, he said.
The inquiry also heard from another former child migrant, Oliver Cosgrove, who is now in his late sixties and who also lived at Castledare.
He said the Christian Brothers, who ran the home, would visit the children's beds at night.
"We were told at Castledare that we always had to sleep on our right hand side so that the heart was closer to heaven," he said.
Brother Murray had fondled him and had also "come to my bed and forced me to give him oral sex," the Inquiry was told.
Mr Cosgrove only fully remembered some of the abuse in 2014 after reading documents connected to an Australian abuse inquiry.
He said: "The memory of this caused me to have several days of sobbing in my apartment, the apartment walls are not very thick. I used to drive down to a riverside reserve which is nearby and just sob for several hours in the night."
How will the inquiry work?
The first phase of the Independent Inquiry into Child Sexual Abuse is looking at the way organisations have protected children outside the UK.
Between 7,000 and 10,000 children were moved from the UK to Australia after World War Two.
They were recruited by religious institutions from both the Anglican and Catholic churches, or charities, including Barnardo's and the Fairbridge Society, with the aim of giving them a better life.
The inquiry, now into its third day, will hear testimonies from child migrants over a fortnight.
Rotherham United have appointed their former player Richie Barker as assistant to manager Paul Warne.
[NEXT_CONCEPT]
A former child migrant, sent from Wales to an Australian orphanage, has told a child abuse inquiry how it was a "feast of kids" for paedophiles working there.