A long-delayed free trade agreement between the U.S. and South Korea came into effect Thursday, amidst protests in Seoul over the one-sided nature of the pact.

The agreement, originally signed in July 2007, was only ratified by the U.S. Congress after a renegotiation to address complaints from the American auto industry.

The deal is the biggest for the U.S. since The North America Free Trade Agreement (NAFTA) was signed in 1994 and means that export-dependent South Korea now has free trade agreements with the world's two largest economic areas, after a pact with the European Union came into effect in July.

U.S. President Barack Obama called his counterpart Lee Myung-bak in Seoul to welcome the deal on Thursday, which is set to boost trade between the two allies by up to $6.9 billion annually according to the U.S. International Trade Commission.

According to the Yonhap news agency of South Korea, President Lee said in a statement:  I expect the implementation of the Korea-U.S. FTA will contribute to advancing economic development and strengthening relations of the two countries.

Korean opponents of the deal say it serves big business at the expense of farmers and the country's service industry, according to Agence-France Presse.

On Wednesday around 1,200 protesters demonstrated against the deal just hours before it came into effect.

Proponents of the deal also rallied in support of the pact which will scrap custom duties on thousands of items.

Hundreds of people gathered outside a Seoul train station Thursday, holding placards with slogans such as Let's occupy the world market and become an economic power, Agence France Presse reported.

According to data from the Korea Customs Service, trade between the two nations was worth $101 billion in 2011, up $11 billion from the previous year.