Heading to Madrid in late September - should we purchase tickets for El Prado in advance?
Our host recommends buying in advance on this website, which costs a little more but will probably save time in line. You have to specify a date but not a time. If you can't commit to a particular day, he suggests going at lunchtime, and weekdays instead of weekends, for smaller crowds.
I successfully avoided a ticket buyer's line by buying tickets on site at the end of the day, for a future entry. You do have to specify the date you want the ticket valid for, so make sure you get it for the date you want.
Assuming you want to enter early in the day, that's when the ticket lines can be long, so you do want to buy in advance, whether at the ticket window or online.
If you are going to the other museums, you may want to consider getting the museum card. At the Prado, we went to a special window (with a much shorter line than regular sales) at the box office to get our tickets and then got in without any issues (we arrived around 10:40 a.m. on a Thursday in May).
If you're on a budget Prado has free entry Monday-Saturday 6-8 and Sundays 5-7. You'll want to get there at least 15 minutes early to beat the crowds. However, if you're someone who is very interested in art you won't want to do this because it's a big museum and two hours won't be enough time!