The weather in the Cusco region is different from some other parts of the World. We have 2 seasons, the dry season and the rainy season. The rainy season begins usually in December and last until April. May through November is dry season. That does not mean that it never rains in the dry season but it is mostly dry with an occasional light shower.
In the rainy season, we have heavy tropical showers frequently. The Cusco region has a tropical high mountainous type of weather. That means our weather can change quickly from sunshine to a rain shower within a few minutes. A few clouds form (usually in the afternoons), it rains for a few minutes and then out comes the sun again. We do not usually have rain all day long, only occasionally in the rainy season. The weather reports are very misleading. It can show that it is raining every day; but all that means is that somewhere in our mountainous region there will be a shower. It can be rainy in one area of Cusco and completely dry in another area.
On the Inca Trail the weather depends on whether it is the rainy season or the dry season. The 1 and 2 day Inca Trail is at lower altitude than Cusco, 1,000 meters or about 3,000 feet lower. Thus it tends to be a bit warmer during the day and at night.
However, it is more tropical and more humid than Cusco. There is always a chance of a rain showers but in the rainy season these showers will last longer and be much more intense tropical rain showers. The Inca Trail is made of stones laid in the ground so it can be more slippery to walk on in the rainy season.