"We've long worked with Kobalt to help creators get paid quickly and more accurately," Christophe Muller, YouTube's global director of music partnerships, said in a statement. "Our deal with AMRA takes this work another step forward to ensure that artists, songwriters and publishers get the maximum value from YouTube."
The video-hosting site said in the last few years it's generated more than $1 billion in revenue for the music industry. Existing Kobalt clients are already integrated into YouTube in the United States, the music publisher said.
The YouTube deal follows a similar agreement announced in August between AMRA and Apple Music.
Read MoreAdele gives fans a long-awaited 'Hello' in new single
"Kobalt is a proven expert in harnessing automation. This type of royalty-payment automation speeds up the payment of streaming revenue to music rights holders. This is welcomed by rights holders, who have a love-hate relationship with YouTube," Catherine Moore, a music business professor at New York University, said in an email. "YouTube is where more people stream music than anywhere else, free of charge. People are willing to watch ads to get access to the videos for free. The ways the ad revenue is split vary from artist to artist and label to label."
"Music rights holders don't know what to make of YouTube: they want the huge and viral exposure that YouTube provides, but they would like to have YouTube act more like a traditional music distributor," she said.
During Alphabet's conference call last Thursday, Google CFO Ruth Porat said YouTube revenue is growing at a "significant" rate. The video site said Wednesday it is seeing 40 percent more advertisers year over year and is launching a new subscription service called "YouTube Red" without ads.
Read MoreYouTube offers ad-free videos...for a fee
Google Ventures led a $60 million Series C funding round for Kobalt in February.