When you open a Lonely Planet you will most likely find several possibilities of getting to Cuzco and Machu Picchu. The one I want to describe here is a less common one and at least when I did this trip back in 2005 I couldn’t find any reference on how to do it.
My journey started from Rio Branco in the Brazilian Amazon where I happened to do a part of an internship at the German Development Cooperation
within the Rainforest Conservation Project ProManejo of PPG7 back in 2005.
There was a bank holiday weekend and I quickly decided to take the opportunity to get to know the Inca ruins of Cuzco and Machu Picchu.
From Rio Branco one has to take a group taxi (taxí de locação) to Brasiléia and then another one from there to Assis Brasil. The total journey should be around 5 hours including changing the car and finding new passengers and should cost around R$ 40. Then in Assis Brasil you can change the border to Peru by foot crossing a small river. On the other side you can then take another group taxi to Puerto Maldonado which was, if I remember correctly, 35 Soles and took around another 5 hours.
I then stayed the night in Puerto Maldonado, departing early on the next morning on a short flight from Puerto Maldonado to Cuzco which was around US$ 80. The next three days I enjoyed Cuzco and Machu Pichu where I went by train (there was a cheap train where most passengers were native Spanish speaking tourists and a more expensive one).
On my way back I left Cuzco on a flight to Puerto Maldonado at around 10 am and managed to get back to Rio Branco at 10 pm in the evening.