The NATO member will spend 2.8 billion koruna ($120 million) on the missiles made by Israeli arms maker Rafael, which are due to be supplied by October 2027.
The missiles can destroy drones, helicopters, airplanes and missiles in a range of up to 80 kilometres (50 miles) and at a height of 20 kilometres.
"The war in Ukraine has shown the importance of defence against attacks from the air, be it drones or standard air force," Defence Minister Jana Cernochova said in a statement.
The I-Derby missiles will complement four Spyder short-range air defence system batteries made by Rafael, which Prague will receive under a 2021 contract worth $630 million, the defence ministry said.
The deal on the missiles is due to be signed by the end of the month, it added.
The Czech Republic has provided Ukraine with substantial military aid since Russia's invasion.
It has pledged to raise its defence budget to two percent of gross domestic product, as required by NATO, from 2024.
In September, it signed a $6.5 billion deal to buy 24 US-made F-35 fighter jets.
The Czech Republic fosters close ties with Israel as one of its staunches allies in Europe.
Czech Prime Minister Petr Fiala is currently visiting the country to express support as it reels from the deadly October 7 attack by Hamas militants.
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