Climate in Peru in September

I have stayed in Cuzco in September and unless you are in a high end hotel figure that your room will not have heat or double glazed windows for the cold nights and that you may what to wear clothes, hat and gloves to bed. In general because it can be hot in the day and cold at night layers are good. The sun is very strong here due to the high altitude and nearness to the equator so you may want a sunhat and sunscreen. I have got bad sunburn for even 20 minutes unprotected.

Most days in September in Cuzco are sunny with blue skies and hence hot but if you do a cloudy day figure it will be colder. There are very few days with rain in September as it is part of the dry season (April - October approx). In fact the climate here does not have 4 seasons like the East Coast of US, but 2 - dry and wet. You can read more detail in the wikipedia article on Cuzco climate

It is very easy to buy clothes inexpensively at the Molino market in Cuzco which is next to the bus station or at many other places in town so I wouldn't worry too much about bringing the perfect clothes. Note that prices outside of the tourist areas of Plaza de Armas and San Blas are significantly lower for clothes, lunch or anything else. In the case of lunch it could be USD $1 for 3 course lunch at a Peruvian place vs $20 in the tourist areas in an upscale place, and $5 even in a "cheap" place.

I have found South American Explorers, a non-profit for travelers to Peru and other South American countries, to be very helpful too.

Cusco:

High: 70F Low: 40F

This is just before the rainy season (Dec-Mar) and crowds are general less. The nights can be rather chilly so dress in layers that you can take off.

Lima:

High: 70F Low: 60F

The weather in Lima is much more regulated. You may see light rain in the late afternoon/evenings.

Lake Titikaka:

I've never been to Lake Titicaca, it seems like it's mostly dry and warm during the day with night time temperatures getting cold.

I visited Peru in August, starting from Lima and touring for three weeks. In my experience, Lima's weather was pleasant bordering on the hot, and even the evenings were normally temperate.

We went to the Andes, first in Huancayo and Ayacucho, where temperatures were 25°C in daytime and got cooler in the evenings; something similar was to be found in Juliaca and Puno (lake Titicaca) and in Arequipa.

The coastal area (Nazca, Ica, Pisco) was not different from Lima, so we never had to wear pullovers or similar garments.

Cuzco was a different matter. Despite the fact that it is not so very high in the mountains, Cuzco proved to be rather cold in the evening and we actually needed sweaters and even woollen gloves. Luckily you could get beautiful alpaca garments at a very reasonable price.

We never spent the night in tents or sleeping bags (we were travelling with an eight-year-old child) but had no problem in finding inexpensive hotels and hostels, which we tried to book over the phone one day in advance. Lima is perhaps the only place where advance booking is really advisable, also because of the fact that some areas of the town may prove distinctly dangerous and you may prefer to stay clear of them.

(Facepalm) When I read this, I didn't register you'd said September. I was actually there in late September/early October (as well as briefly in August).

I don't remember being really cold, ever, which was different to Bolivia where it was FREEZING (below freezing) at the Salt Flats.

I assume if you did the Inca Trail you'd camp outside and get cold though - the temperature and oxygen drops dramatically as you go up. But the day I was on Machu Picchu it was hot, and I was in t-shirt and shorts (checks - it was October 4).

Lake Titicaca has a weird climate - in Puno, with a chance of a Thunderstorm in the late afternoons as the muggy weather changes. It was cool in the evening, but not cold.

I make fun of my friend from Lima by saying it's always 18C and semi-misty when I've been there. Turns out this isn't far from the truth, the Humboldt current causes it to almost always be cool as it brings the colder air in from the south, which surprises people who see it being close to the equator.

Mancora on the other hand - hot. On the beach, ALL day. Brilliant :)

Michael Smith's comment about Cuzco (and indeed Lima) is true - it's easy to buy warmer clothes - cheaply, just don't buy in the main squares. And baby alpaca wool is NOT actually from a baby alpaca - but it works well for selling to tourists ;) However the garments are all pretty good, and genuinely warm, I still use my jersey two years on.

I'm from Lima and I can help you with some info.

Lima
About 18 - 20 ºC
Lima is pure humidity, be careful of asma problems.

Cusco
sunny ocassionaly 20 ºC at day - 1 ºC at night Ice winds too, but not so much.

Puno Ice winds, you're at 3800m sea level
13 ºC - -5 ºC

Ancash - Huaraz Ice winds, you're at 3400m sea level [69 Lake 4600m sea level, almost die there, i forgot taking a jacket :( ]
23 ºC - 11 at night ºC

Notice when in Lima is cold, all highlands are in Summer and spring season. Have a nice trip!