Buddha Air shows flights for $250 for a round trip in late November.
Local travel agents can book tickets but you can also book directly on some airlines' websites e.g. Buddha Air but not Nepal Airlines.
I would book in advance to avoid flights being booked up when you want to fly. This depends on how long you will be in Nepal before flying to Pokhara and whether its's low or high season (to some extent).
Flight fare from Kathmandu to pokhar and return costs $250 but some agency offers some discount on that price.
Booking with agency is recommended than from airlines website cause you can get some discount and easy process with agency.
Thank you.Edited: 13 November 2018, 23:04
There are 2 airlines I know which operate domestic flights within Nepal. One is Buddha Air and another is Yeti Airlines. You can book the tickets on the website, it's quite reasonable. Travel agent site might charge more.
Here is the link of website: