As it happens, Wikitravel actually has an article titled Pontianak to Kuching:
Traveling from Pontianak, the capital of West Kalimantan province in Indonesia to Kuching, Sarawak, Malaysia, or vice-versa, in a day can be easily done by flying, driving, or by catching buses. Of course, the level of comfort, and how much you end up spending, will depend on what mode you choose.
The article discusses the various modes of travel between the two points, including plane — and Batavia Airlines is cited.
The fastest and most comfortable [method of traveling from Pontianak to Kuching], but also the most expensive is through Batavia Airlines  which operates four flights weekly and Kalstar Aviation which operates daily flight between Pontianak and Kuching. The flight takes about 40 minutes. There is also talk about Air Asia and MAS Wings potentially servicing this route.
As a July 24, 2012, edit to this post, some of these further variously-related references may be of interest or use to you. Many are fairly old — if that is of significance, then just look for the publishing date and pass the links by. Sometimes older articles can be illuminating when taken from the perspective of the present:
… hours drive from Kuching while air travel takes 40 minutes. Indonesian airlines such as KalStar Aviation and Batavia Air serve the Kuching–Pontianak route and Malaysia Airlines’ subsidiary, Maswings, has introduced its services in this region. … Maswings began operating the route on Feb 6 and serves 17 flights weekly, compared to daily flights by KalStar Aviation and three times weekly by Batavia Air from Pontianak. “Our entry to the market has increased the seat …
Publish Date: 03/01/2012 1:36
The others are Malaysia Airlines, Air Asia, Firefly, Batavia Air, Royal Brunei Airlines, Tiger Airways and Silk Air. Kalstar commenced scheduled daily flights for the Jakarta-Pontianak–Kuching and vice versa route with arrival in …
Publish Date: 05/24/2011 3:09
Currently the only flight from Indonesia to Sarawak is a Batavia Air flight from Jakarta to Kuching, via Pontianak. According to the Pontianak Airport Wikipedia page, Malaysia Airlines is awaiting statutory approval to also fly …
Publish Date: 06/05/2011 14:12
Kuching (Malaysia) has a direct flight to Pontianak and Riyadh (Saudi Arabia) can be reached from Jakarta by Batavia Air. Earlier this week, ticketindonesia.info also launched actual ticket prices. With this new website, …
Publish Date: 02/15/2011 20:12
Others airlines operating at KIA are Malaysia Airlines, Air Asia, Firefly, Batavia Air, Royal Brunei Airlines, Tiger Airways and Silk Air. Kalstar commenced scheduled daily flights for the Jakarta-Pontianak–Kuching and vice versa …
Publish Date: 05/24/2011 0:48
Ang Kian Guan, BIMP-EAGA chairman for transport, infrastructure and information technology, said airline executives were joining the meeting to discuss the possibility of adding more intra-regional flights. At present, there are only five airlines connecting the major … Airlines and Davao-Kota Kinabalu by Cebu Pacific Air. Other proposed routes are Kuching-Bandar Seri Begawan-Kota Kinabalu by Air Asia and Pontianak –Kuching– Bandar Seri Begawan by Batavia Air.
Publish Date: 03/05/2008 0:35
It will operate one flight daily between Kuching and Pontianak in West Kalimantan from Feb 6 and three flights a week from Tawau to Tarakan in East Kalimantan beginning Feb 13. Bolkiah said statistics from his ministry showed that … Silibus islands and Mindanao by year-end, he said. Previously, only Royal Brunei Airlines served the Kota Kinabalu-Bandar Seri Begawan route while Indonesia’s Batavia Air and Kal Star Aviation operated the Kuching–Pontianak route.
Publish Date: 02/02/2012 14:31
… to Pontianak (the capital of West Borneo province). The flight takes one hour and fifteen minutes. There’re some airlines with many options of time departure everyday: Batavia Air, Garuda Indonesia, Sriwijaya, Lion Air and Mandala Air Service, with tickets start from Rp.400000,- to Rp.900.000,- in normal season. … From Kuching, take the bus to Pontianak. There’re some options of buses: SJS bus, Damri bus, or bus owned by Malaysian company. The ticket is about …
Publish Date: 07/03/2009 3:34
Somebody told me that Malaysian Airlines would fly from Pontianak to Kuching but i didn´t find anything from the website.. Thanks if you help! … I found airline called Batavia Air, they fly from Pontianak to Kuching. I will try that.
Publish Date: 01/11/2008 2:43
… Hong Kong, and Pontianak. Flights to Kuching are also operated by AirAsia and Firefly. International airlines operating in Kuching includes SilkAir, Royal Brunei, Tiger Airways, and Batavia Air.The airport underwent a major …
Publish Date: 09/02/2011 23:04
Visitors from Sarawak have to cross the immigration checkpoints at Tebedu and Entikong to get to Pontianak. Alternatively they can fly by the thrice-weekly Batavia Air services from Kuching’s International Airport to Supadio …
Publish Date: 09/26/2009 19:06
Kuching Travel Guide Why Not Go Why Go Best Time to Visit Where to Stay Where & What to Eat Nightlife To Do List Stay Away From Getting. … MASwings links Kuching with Mukah and International connections are available, although there are a few weekly services to Guangzhou, Hong Kong, Jakarta, Macau and Pontianak. Others international airlines operating in Kuching includes SilkAir, Royal Brunei, Tiger Airways, Jetstar Airways and Batavia Air.
Publish Date: 08/04/2009 2:00
But have just realised no airline fly this route direct. Anyone … Air Asia through KL would be an option (would need to by 2 tickets though). Share … If you are adventurous you can fly Batavia Air from Bali-Pontianak–Kuching.
Publish Date: 12/22/2009 19:25
Apparently there’s only Batavia Air that services the Kuching–Pontianak route with the exception of the bus services that’s daily. So anyways, Banie came from Sabah on Sunday with the knowledge that our tickets had already …
Publish Date: 03/19/2007 21:51
Batavia Air. Flight between Kuching and Pontianak & Jakarta (Indonesia). Tel : 082- 244299 (res), 628166 (airport counter), Fax : 082-240266. Web : www.batavia–air.co.id. Hornbill Skyways. To book a helicopter for a joy rides and sightseeing Tours or filming and special … then head off to sandakan, to the orang utan sanctuary! take a bus, or a flight with airasia.com, now they have 1(0ne)MYR ticket airfare offer, really cheap! if u book it now for Aug you can still get it!
Publish Date: 06/16/2008 0:00
pontianak to kuching with batavia airline
Uploaded by hokkaidoyakitori on Jul 8, 2010
a very short journey…