Is there direct flight from Prague to Budapest?

You didn't say when so I just picked a random week in May on the Ryan site (started with Google flights) and there are 2 a day for $28 to $40.

If you are looking way out, the discount carriers often don't schedule as far out as other airlines... so wait a while

No personal experience flying that route, but it depends on the day of the week, and what month you're traveling - it's seasonal. Looks like right now, flights are Mondays and Fridays; flight frequencies increase starting end of March, and go 6 days a week from April through October (all flights seem to end in late October).

If the flights do not work, there are direct trains between the two cities. At 6-7 hours, they take longer than a direct flight, but not longer than a connecting flight!

Thank you for the responses. After looking closer at the Ryanair website, I realized that it was set on the UK instead of the US site. I can see the direct flights after I switched to US.

We took a bus from Prague to Budapest. It was quick, easy, clean and cheap. Highly recommend!

Ryanair is the only airline flying that route. I didn't check to see if it's flown daily. Often they just fly certain days of the week--not every day.

There will be train service from Prague to Budapest. City center to city center. Inexpensive, no security lines, no transit to/from airports, etc. Multiple direct high-speed trains per day, as low as $35. Show up at the train station about 20 minutes prior to departure (to leave yourself some buffer).

Unfortunately, there is no "High Speed" train.
It averages not more than 55 mph and takes not less than 7 hours or about the same as a flight from JFK to LHR.

But the train is much more romantic than the 1:10 flight. https://community.ricksteves.com/travel-forum/czech/prague-to-budapest-transportation-options