There are multiple options for residents of Malaysia to travel to Bhutan by first travelling to the various port of call of Drukair, Royal Bhutan Airlines.
Traveling to Bhutan via Kathmandu in Nepal.
There are many airlines that provide air services between Kuala Lumpur (KUL) and Kathmandu (KTM) on a daily basis. These airlines include Malaysian Airlines (MAS), Malindo, Air Asia X, Himalayan Airlines and Nepal Airlines which together provides up to 4 flights a day between KUL and KTM.
Malaysian travellers typically will have to lay over one night in Kathmandu and catch a Drukair flight from KTM to Paro (PBH), Bhutan.
Traveling to Bhutan via Bangkok in Thailand.
There are more than 20 flights a day between KUL and Bangkok (BKK).
Do note that Drukair departs BKK from Suvarnabhumi Airport twice daily and travellers from Malaysia should be able to catch an early morning flight to Suvarnabhumi and connect with Drukair's afternoon flight from (May til Feb)
Traveling to Bhutan via Singapore on Drukair.
Singapore as a port is also an option for many Malaysian especially if they are staying in the southern state of Johor and Melaka. Travelling by road to Singapore, travellers can catch the twice weekly direct flight from Singapore to Paro
Singapore Paro route was introduced by Drukair in September 2012. The route would include a stop over in Guwahati, Assam, India. You will not require a Indian transit Visa as passengers who are enroute to Paro do not have to disembark from the plane during the stopover.
Do Malaysian Nationals need visa to visit Bhutan?
Yes, Malaysia passport holders require a visa to travel to Bhutan. A physical copy of the Visa must be produced during check-in for your Bhutan bound flight. Your Bhutan visa is granted for one time entry for the duration of the travel only. So a traveler seeking a one week stay in Bhutan would be granted a one week stay beginning on the departure date. Tourist visa can be obtained from authorized travel agency like Druk Asia - Bhutan Travel Specialist.
Please visit Bhutan Tourist Visa Application Procedures
