The National Day of Prayer is intended as a time for Americans to put aside differences and unite behind a shared appreciation of faith, but that is tough to do in a country increasingly divided over religion.

Americans in all 50 states gathered in churches, schools and parks on Thursday to pray for the nation. This year’s theme was “unity,” citing the Bible’s Ephesians 4:3: “Make every effort to keep the unity of the Spirit through the bond of peace.”

Pastor Ronnie Floyd, president of the National Day of Prayer Task Force, said prayer still has the power to bring the country together, but only if accompanied by repentance and humility. He cited the national prayer issued by President Lincoln at the height of the Civil War, in which he called on Americans “to humble ourselves before the offended Power, to confess our national sins, and to pray for clemency and forgiveness.”

“The act of repentance in prayer is what brings us together,” Mr. Floyd said. “If America repents, if we recognize that we’ve allowed hatred and division to take root in our hearts and we turn to God in honest, humble prayer, there can be unity in our country.”

The National Day of Prayer was established in 1952 by a joint congressional resolution signed by President Truman, an effort to further distinguish America from the officially secular Soviet Union. President Reagan amended the holiday so it would fall on the first Thursday in May.

For the second year in a row, Mr. Trump signed an executive order reiterating his administration’s commitment to religious liberty.

Last year, the order announced his willingness to rescind the Johnson Amendment, which restricts churches and religious groups from contributing to political campaigns. This year, the administration launched a White House Faith and Opportunity Initiative that, among other things, tracks any “failures of the executive branch to comply with religious liberty protections under law.”

“The faith initiative will help design new policies that recognize the vital role of faith in our families, in our communities and in our great country,” Mr. Trump said in remarks in the Rose Garden. “This office will also help ensure that faith-based organizations have equal access to government funding and the equal right to exercise their deeply held beliefs.”

While America’s faithful view the National Day of Prayer as a moment of unity and togetherness, some secular Americans see it as a day of discord and division.

Rachel Laser, executive director of Americans United for the Separation of Church and State, accused the president of using the occasion to “divide and discriminate.”

“Our government should protect religious freedom, not use it as a sword to harm others,” Ms. Laser said in a statement. “Our country is strongest when we are all free to believe, or not, as we see fit and to practice our faith without hurting others.”

The White House held a reception on a sweltering morning in the Rose Garden to mark the National Day of Prayer.

Members of the Hope Christian Church choir opened the festivities with hymns accompanied by a piano. Faith leaders from various sects were invited on stage to bless the gathering.

Vice President Mike Pence and Mr. Trump delivered brief remarks to the small audience of religious dignitaries, including Christian author Eric Metaxas, televangelist Paula White, baseball legend Darryl Strawberry, who founded an addiction ministry after his playing days, and Cissie Graham Lynch, granddaughter of the late Rev. Billy Graham.

Mr. Pence encouraged Americans to step away from politics to pause and pray. He said prayer is part of the American character and an invaluable resource in these “too-divided times.”

“You know, the sweetest words the president and I ever hear are the words, ‘I’m praying for you,’” the vice president said. “And we hear it a lot. But that’s really nothing new. The American people believe in prayer. Always have. Prayer is the chord that runs through every era of America’s history.”

There is evidence that religious and political divisions go hand in hand.

Research published last month by Gallup found states are divided not just by their support for Donald Trump or Hillary Clinton, but also by their religiosity. Red states in the South and Midwest tend to have higher rates of belief, the study found, than blue states on the coasts.

In the most secular part of the country, New England, 48 percent of residents described themselves as “not religious,” compared with 26 percent who said they were “very religious.” In the Pacific states of California, Oregon, Washington and Alaska, 43 percent of residents said they had no faith.

Religiosity was highest in the South, where more than 40 percent described themselves as very religious and about one-quarter said they were not religious.

Gallup also found last year that 51 percent of the highly religious, compared with 32 percent of the nonreligious, had favorable views of Mr. Trump’s performance in office.

A Pew Research Center study published last week found that 70 percent of Republicans or Republican leaners believe in God “as described in the Bible,” compared with 45 percent of Democrats and Democrat leaners.

An observance was held in the Capitol Thursday night to mark the National Day of Prayer.

In attendance was Frank Pomeroy, pastor of First Baptist Church in Sutherland Springs, Texas, where 26 people, including the pastor’s 14-year-old daughter, were killed in a mass shooting last year.

Shootings like the one in Sutherland Springs have exposed a rift in America over prayer. Elected officials and others in favor of gun control often mock the idea of sending “thoughts and prayers” to those afflicted by tragedy.

Mr. Floyd, the National Day of Prayer president, said that reaction relies on a misconception of prayer.

He said prayer is often treated in an “utterly pragmatic way,” that it’s only about “asking God to do something for us,” that people put prayer “aside during the good times and only turn to it as a final alternative in the bad times.”

“The issue with sending ‘thoughts and prayers’ after a tragedy is not that praying is a form of inaction or avoidance of reality,” Mr. Floyd said. “In fact, I believe prayer is our greatest action. The problem is that we haven’t valued prayer more. We haven’t turned to God as we walk throughout our days and sought his wisdom and counsel so we may live in a right way before him and each other.”

Read more at National Day of Prayer seeks to unify U.S., but some say it sows discord and division.