Wearing royal blue, the monarch arrived at St Mary Magdalene Church, close to her Sandringham estate on Sunday morning.
She had missed her regular appearances on Christmas Day and New Year's Day because of the lingering respiratory illness.
The Queen was greeted by a small crowd of people as she was driven the short distance to the church in a burgundy Bentley, accompanied by Philip, who also suffered illness over Christmas.
The Queen at Sandringham - in pictures
One man told the BBC: “We saw her very close up. We have been waiting the past three weeks to know she has attended. It is very nice to see her and of course, Prince Philip too.”
The Duke and Duchess of Cambridge also attended the service after walking the short distance from the house to the church but there was no sign of Prince George or Princess Charlotte.
Although she has missed the church services, and has not been in seen in public for several weeks the monarch has carried out other duties.
She presented Ray Wheaton, her Page of the Chambers, with the insignia of a Lieutenant of the Royal Victorian Order, the court circular recorded.
Her Majesty and the Duke of Edinburgh had been forced to delay their journey from Buckingham Palace to their Norfolk estate in the days before Christmas after she fell ill.
