JUBA, Sudan—A huge digital clock looms in a traffic circle in this dusty capital, counting the days, hours and minutes until Jan. 9, when people here will vote on whether to split Africa's largest country in two.

After decades of civil war, and several years of tenuous peace, southern Sudan is preparing to decide whether to split from the north to form a separate nation. Southerners—mainly animists, adhering a traditional African belief system, and Christians—are widely expected to choose secession from the predominantly Arab Muslim north.

The stakes for both sides are huge. Southern Sudan has fertile agricultural land and most of the country's oil, which is pumped through a pipeline to the north, where it is refined and sold. Losing the southern region to secession could be a financial blow to President Omar al-Bashir, whose regime has been enriched by oil revenue.

How the south handles the vote, and its expected nationhood, will reverberate through a resource-rich region that includes war-torn Somalia and the turbulent Democratic Republic of Congo. A stable southern Sudan could galvanize investment in the area; instability could set back the pace of development.

Recent comments from the government in Khartoum, the Sudanese capital in the country's north, have spurred hopes that the potential split would be peaceful, but secession is fraught with risks.

A few months ago, the referendum faced delays amid logistical challenges, such as setting up an electoral commission and printing ballots. But now all appears on schedule for the week of voting to start Jan. 9.

"It's a very big moment for Africa," said Greg Mills, author of "Why Africa is Poor: And What Africans Can Do About It."

A 2005 peace deal that ended Sudan's last civil war, which cost about two million lives, provided for the referendum. That deal was signed by President Bashir, who is wanted by the International Criminal Court for alleged war crimes related to massacres of civilians in the western region of Darfur, and whose regime, designated by the U.S. as a state sponsor of terrorism, is subject to tight economic sanctions. According to a recent count by the election bureau set up by the southern government, some 3.4 million southerners have registered thus far. That is below the 4.7 million the bureau had forecast, but still a high figure given that some people had to walk 65 miles to ensure their name was counted, according to a local election monitoring group. The south has about eight million inhabitants; the north has about 34 million.

Most residents of the southern town of Juba openly advocate secession. Concrete walls and SUVs are plastered with signs bearing a raised, open palm—the symbol chosen by the electoral commission to represent separation on the ballot.

The symbol for unity—two hands clasped in greeting—is rarely visible. Rather than shaking hands, some southern Sudanese greet each other with a high five—to represent separation.

"It will be far better, simply because I am assured of my freedom, of my safety," said William Bokut, a 47-year-old baker. Mr. Bokut recently returned to Juba from the north, where he had scraped out a living for several years amid what he said was harassment and discrimination for being a southerner.

The north and south, which share oil revenue, likely would have to settle on a deal—at least temporarily—to share the funds if they separate. That could help ensure peace, as neither side wants to endure an interruption in the oil flow.

But after months of negotiations, contentious points have yet to be resolved. The official north-south border has yet to be defined. And if the south votes for independence, the promise of more power and wealth could spark conflict among factions that have now united in their quest for secession.

Another civil war in Sudan could cost more than $100 billion over a decade, and hundreds of thousands of lives, according to a recent study by Frontier Economics, a London-based research firm.

"The date [of the election] has become sacrosanct for the aspirations of Southerners here," said Jasbir Lidder, a top official with the United Nations mission in Sudan.

An immediate concern, however, is interference from the northern government ahead of the vote. The U.N. has confirmed that southern Sudan had been bombed along its unofficial border with the north in recent weeks. Khartoum has denied it carried out the attacks.

In the past six months, the U.S. has tripled the number of diplomats working in Sudan, stepped up visits by senior officials, and spent $162 million on efforts including job training for Sudanese youths, resolving conflicts over resources and providing election security. U.S. sanctions on agricultural equipment for the entire country have been lifted. All other sectors remain under U.S. embargo. The United Nations is also paying $220 million annually toward the cost of a 20,000-man U.N. peacekeeping force in the south.

This month, Mr. Bashir's northern government offered a sign that it may be willing to accept secession. A presidential aide said the south's separation "has become something expected," according to Sudan's state news agency.

Mistrust of the north remains deep among southern Sudanese. Acuil Banggol, an official for the Sudan People's Liberation Movement, the ruling party in the south, said the north "had been planting seeds of discord, and then they wanted to harvest good fruit—it's not possible."

For separation to pass, it must win 60% of votes cast. A study of southerners by the U.S.-based National Democratic Institute found that "the vast majority of participants indicate they will be voting for separation."

"We are confident people will vote, and we are confident people will vote for separation," said Lokulenge Lole, chief coordinator of a civic education group that helped set up the clock in Juba.Meanwhile, frequent power cuts often cripple the referendum countdown clock. When it stops, motorcycle taxis call up Mr. Lole, who helped to set up the clock, or a colleague. They go out to the sign and switch it back on.

—Joe Lauria in New York and Peter Wonacott in Johannesburg contributed to this article.