Retired Air Chief Marshall Alex Badeh denies 10 charges of fraud, criminal breach of trust and money laundering.
He was appointed chief of defense two years ago.
ACM Alex Badeh is accused of using the funds to buy a mansion in the capital Abuja along with a string of other properties.
More than $1 million in cash was also reportedly found at one of his homes.
Under former President Goodluck Jonathan, front-line troops complained that they were ill-equipped to fight the militants and discipline in the army was breaking down as soldiers refused to carry out orders.
An investigation has alleged that a total of $2 billion meant to buy arms to fight Boko Haram had gone missing.
The former national security adviser, Sambo Dasuki, was charged in December in connection with the case involving $68 million that is alleged to be missing. He was accused of awarding phantom contracts to buy helicopters, fighter jets and ammunition, which he denied.
Twelve other senior Nigerian army officers were handed over to the anti-corruption agency in February for their alleged involvement in the arms scandal.
Muhammadu Buhari won elections a year ago on promises to tackle both Boko Haram and corruption.
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