Cusco has a temperate climate with year round temperatures fluctuating between 14º - 16ºC, with warm days and cold nights. The rainy season in Cusco is from December to March.

Machu Picchu has a semi-tropical climate, with warm and humid days and cold nights.
The rainy season in Machu Picchu is from November to March, so be prepared.
The wet months are January to April, when roads are often closed by landslides or flooding.
The best months for visiting Machu Picchu are from April to October.

The Inca Trail begins on a zone called "Quechua": This zone is between 2300 - 3500 m (7,500-11,500 ft) and its weather is temperate and dry with temperatures that range from 0 -21C (32 -70F). The rainy season is from December to March. The rest of the year is dry or even parched from May through September. This region is widely cultivated and essentially, there is no natural plants left.
 

Above Wayllabamba, there's the zone called "Suni" or "Jalca": This is the zone between 3500 - 4000 m (11,500 - 13,000 ft). There is still some agriculture possible at this altitude. Above that lies the "Puna" which is a zone from 4000 - 4800 m (13,000 - 15,750 ft). Its weather is very
cold with frequent frost. It is mostly grassland with a type of grass called "Ichu" and the area
is used for grazing camelids like Llamas and Alpacas.

Going down from the "Puna" through the "Suni" is the "Yunga Fluvial": which are inter-Andean valleys on the east of the Andes between 1000 - 2300 m (7,500 - 3,300 ft). These valleys have a moderate, moist climate and abundant vegetation.

HEIGHTS
Cusco City: 3,360 m.a.s.l.
Machu Picchu: 2,400 m.a.s.l.
Urubamba Valley: 2,850 m.a.s.l.
Inca Trail highest point: 4,200 m.a.s.l.
 

Temperature variation in Cusco through the year

Rainfall variation in Cusco through the year