In her address, which was broadcast on TV, radio and social media, she thanked everyone on the NHS frontline.
"I am sure the nation will join me in assuring you that what you do is appreciated and every hour of your hard work brings us closer to a return to more normal times," she said.
There are thanks from the Queen too for "those of you who are staying at home" and by doing so, "helping to protect the vulnerable and sparing many families the pain already felt by those who have lost loved ones".
She said: "Together we are tackling this disease, and I want to reassure you that if we remain united and resolute, then we will overcome it."
The Queen said it has been a time of compassion.
"Across the Commonwealth and around the world, we have seen heart-warming stories of people coming together to help others, be it through delivering food parcels and medicines, checking on neighbours, or converting businesses to help the relief effort," she said.
She adds that it has become a time of reflection for some as well.
"Though self-isolating may at times be hard, many people of all faiths, and of none, are discovering that it presents an opportunity to slow down, pause and reflect, in prayer or meditation."
The Queen said people will look back with pride and our generation will be seen as a strong one.
"Better days will return... We will be with our friends again, we will be with our families again. We will meet again."
The Queen's message was filmed by a single cameraman wearing protective equipment, with all the other technical staff in another room.
The address comes less than a week after the Prince of Wales came out of self-isolation, following his diagnosis of coronavirus.
Prince Charles, 71, spent seven days self-isolating in Scotland after testing positive and displaying mild symptoms.
On Friday, he opened the NHS Nightingale Hospital in London via video link.
Buckingham Palace previously said the Queen last saw her son, the heir to the throne, on 12 March, and was "in good health".