AIR PIA is oprating flights to chitral flights from Islamabad & Peshawer daily.
When the passes are open, microbuses run from Pershawer to Chitral. The journey takes around 12 hours and crosses the Malakand and Lowari passes. The route will often be closed in winter due to snows. Direct buses only run at night. If you travel during the day you will have to change buses at Dir.
Shared jeeps run from Chitral to Mastuj and Chitral to Khot Valley from where it's possible to pick up the NATCO bus to Gilgit. This will require a night in Mastuj.