Three of his former health ministers will also be indicted, the country's chief prosecutor said.
Around 300,000 women had surgery as part of a government programme during Fujimori's 1990-2000 presidency.
It was meant to be voluntary, but thousands say they did not consent.
Women have reported being harassed, threatened or blackmailed to undergo the procedure.
Most were poor, indigenous women from rural areas.
Over 2,000 people are believed to have filed lawsuits against the sterilisations. Official data states that 18 women died as a result of them.
Fujimori was cleared of any wrongdoing linked to the programme during a previous investigation held in 2014.
The planned charges against him centre on five women who suffered serious injuries during or after surgery, and then died.
The former president, who is 79, was handed a 25-year prison term in 2009 for human rights abuses committed while in office. However, he was pardoned on the grounds of ill-health in late 2017.
The latest developments came as another ex-Peruvian President - Ollanta Humala - was released from prison along with his wife.
The pair have been held in pre-trial detention for the last nine months, while money-laundering charges are finalised against them.
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