It is used in the same way in both countries. It is more common in British usage. In particular, the British sometimes use it as a single-word, to say they agree heartily with something; in the US we would be more likely to say "You bet!" or "You said it!" or one of a number of other expressions. And in the US, "Yes, indeed" is more common than the simple one-word "Indeed."
Here are some examples of US usage:
"An engineer's life: a happy Thanksgiving indeed," from a blog about trains
"Despite record, Razorbacks are indeed a 'really scary team'," from an article about a football team.
"The bottom line is that disinflation is real — indeed, spectacular."--Economist Paul Krugman writing in The New York Times
Q: "If someone wanted to donate to your charity, is there a convenient way for them to do that?"
A: "Yes indeed. Here’s the link."
--interview with the director of a charity