Kyiv's British embassy shared her message as the country celebrated the anniversary in the middle of Russia’s war against the nation.
The day marks 31 years since the collapse of the Soviet Union and Ukraine breaking away from Moscow’s rule.
“On their 31st anniversary of Independence, Her Majesty the Queen congratulates Ukrainians," the UK in Ukraine Twitter account said.
The queen said in her address to Ukrainian President Volodymyr Zelenskyy: "It gives me great pleasure to send Your Excellency and the people of Ukraine my warmest greetings on the celebration of your Independence Day.
"In this most challenging year, I hope that today will be a time for the Ukrainian people, both in Ukraine and around the world, to celebrate their culture, history and identity.
"May we look to better times in the future. Elizabeth R.”
The queen has shown her support for Ukrainian citizens by donating to a charitable appeal.
The Disasters Emergency Committee thanked her in March for making a “generous donation” towards its appeal, set up to help civilians affected by the conflict.
At the time, the palace declined to disclose the amount given.
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Later that month, a photograph was taken during an audience at Windsor Castle with the queen and Canada’s Prime Minister Justin Trudeau, which showed a large bouquet of blue and yellow flowers, the colours of the Ukrainian flag, behind them.
The gesture was seen as a symbol of the queen’s support for the people of Ukraine.