Cusco's climate is divided into two seasons: the rainy season, from November to April (the heaviest rains generally occur between January and March); and the dry season, from May to September.
The rainy season from November to April has a tropical downpour. Heavy, but the rains usually do not last long or the rain is often at night.
Along the Inca Trail (May to September, high tourist season), temperatures range from 15-20ºC (59°F-68°F) during the day if it is sunny, and from 05-10ºC (41°F-50°F) during the day if it is not sunny and from 0-05ºC(32°F-41°F) during the night in between the first and second campsites. In Wiñaywayna and Machu Picchu, which is a subtropical zone, at a lower altitude, temperatures are usually warmer, although warm clothing is still recommended at night.
The Inca Trail is closed for maintenance throughout the month of February. The low season can be a time when you can enjoy Salkantay Trek, Inka Jungle to Machu Picchu without the crowds of people.
As you can see, there is no perfect season (sunny, warm and dry months). So, you have to decide when to do it taking into account your preferences; if the rain bothers you or if you are very cold.
However, to summarize we can say that (from the least good period to the best):
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