Police said they had brought charges against Zia, a two-time former prime minister, and 27 officials from her Bangladesh Nationalist Party (BNP) for their roles in the fire-bombing of two buses in the capital Dhaka.
"We've submitted charge sheets against 27 people including Khaleda Zia to the Chief Metropolitan Magistrate Court," local police chief Mohammad Selimuzzaman told AFP.
"She has been charged as a mastermind in the arson attacks."
His hanging late yesterday sparked several outbreaks of violence and heightened tensions in the Muslim-majority country, already reeling from a string of killings of secular and liberal activists.
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Zia, a bitter political rival of Prime Minister Sheikh Hasina, is already on trial for corruption in a long-running case.
She also faces around half a dozen other charges stemming from her tenure as the premier of the country from 2001-06 -- charges she rejects as baseless and politically motivated.
Earlier this year Zia was charged over a separate deadly fire-bombing of a bus in Dhaka during a nationwide transport blockade she ordered last year in an effort to topple the government.
The blockade unleashed a wave of bloody violence, leaving more than 120 people dead as opposition activists fire-bombed hundreds of buses and trucks, and police responded by firing live rounds.
Zia was confined to her office compound in the capital for months after she threatened to lead an anti-government rally through Dhaka on the first anniversary of a disputed national election.
The BNP boycotted the 2014 general election, leaving the field clear for Hasina's Awami League.
The opposition was further weakened by a government crackdown last year, when police pressed charges against around 15,000 opposition activists over the fire-bombing campaign.