The Prado Museum has five different entrances, each catering to different visitor groups. Puerta de Murillo and Puerta de Goya Baja entrances are typically used by those without pre-booked tickets. Wait times can sometimes range from 30 minutes in the low season to even 2 hours during the peak season between April to June & September to November.
While the museum opens at 10am, crowds start building from around 11am at these entrances, and you’ll find really long queues till around 3 or 4pm.
On the other hand, the Puerta de Velázquez and Puerta de los Jerónimos entrances are reserved for visitors with pre-booked tickets. Wait times, as a result, are a maximum of 30 minutes during the peak season—much better than spending 2 hours in Madrid’s heat, isn’t it?