The Education Secretary said firms are already cutting back on the number of entry level jobs they advertise because they are afraid of what a Brexit could mean for the UK economy.
Mrs Morgan also insisted the Conservatives will be able to heal the deep rift at the heart of their party caused by the referendum campaign but criticised Leave campaigners for making “disingenuous” claims about criminals being allowed to move to the UK from Europe.
Speaking at the Fashion Retail Academy in London, Mrs Morgan said: “We know that it’s young people who will face the brunt of the damage a vote to leave will bring.
“Because the great recession demonstrated the stark reality that when we experience economic shocks, the likes of which we could suffer if we leave the EU, it’s young people who suffer.
“As we saw in that recession, the largest increases in the rate of unemployment were amongst young people. But that shouldn’t be a surprise because when the economy struggles and firms stop hiring, it’s those in the entry level who they stop recruiting first.”
Mrs Morgan warned that a reduction in the number of entry level jobs would mean increased competition for young people.
“It’s clear that if Britain leaves Europe it will be young people who suffer the most,” she said.
Mrs Morgan said that young people want the UK to “choose internationalism over isolation” on June 23 because being in the EU gives the UK the power to “exercise even more clout on the world stage”.
She said: “I want young people to make sure that their voices are heard in this debate, whichever side of the debate that they might be on, otherwise they risk having the decision made by other people.
“Their future decided for them, not by them.”