This is the itinerary I’d recommend following if you had about a month in Kyrgyzstan. It’s for those keen on adding a few hikes and a horse trek across a four-week span.
It covers most of the highlights of the country, plus, a few lesser explored places. The itinerary is broken up into two sections. The first two weeks is spent heading out to the east of the country, before returning back to Bishkek. The second half of the itinerary is about heading south to Osh and the Alay Mountains.
The itinerary finishes in Osh, from where I've allowed for a day to get back to Bishkek to fly out. Otherwise, from Osh, you could also cross over to Uzbekistan if you wanted to keep travelling overland.
This itinerary includes:
Exploring Bishkek, the capital city
Day trip to Ala Archa National Park
Scenic train journey to Issyk Kul lake
Exploring Karakol, the adventure capital
Four day trek to Ala Kul lake
Day trip to Jeti Oguz from Karakol
Staying in Jyrgalan Village
Photo stops at Fairytale Canyon and Aksay Canyon
Staying in Kochkor, base for exploring central Kyrgyzstan
Yurt camp stay at Kol Ukok lake
Heading to Naryn to arrange a trip to Kel Suu
Two night adventure to Tash Rabat and Kel Suu staying in yurt camps along the way
Three day horse trek to Song Kul
Side trip to Arslanbob Valley
Trip to Sary Mogul and Tulpar Lakes in the Alay Mountains
How to travel? This itinerary suits any sort of traveller, whether you're exploring by public transport via marshrutka or hiring a car for your trip. Each of these spots includes information on how to get there, if you need to plan your trip around local transport. You may also have to arrange your own transport or tour for a couple of trips, such as Kel Suu and Tash Rabat (more info is included in the individual spots).
Only have 3 weeks? This could be shortened to a 3-week itinerary if you take out the four-day trek to Ala Kul, the overnight stay in Jyrgalan Village or Kol Ukok lake, and the three day trip from Naryn to Kel Suu and Tash Rabat.