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MCALLEN, Tex. — The 3-year-old boy was alone, and crying.

Early on Tuesday morning, Border Patrol agents at the Fort Brown station in South Texas found the boy in a cornfield. He had his name and phone numbers written onto his shoes. Agents said the boy appeared to be with a larger group of migrants, who fled when the Border Patrol approached.

The lone child crossing the border was not an anomaly — more than 8,900 unaccompanied children were apprehended by the Border Patrol in March, nearly twice the number seen in October.

Many were teenagers, but for years, children younger than 12 have been among those making the journey across America’s southern border without their parents or other relatives, often traveling with groups of strangers. Theirs is a harrowing, complex and dislocating saga, as children as young as 3, 4 or 5 are passed from migrant group to migrant group for days, often eventually abandoned in the deserts of Arizona or in the brush of South Texas.

Like the boy found near Brownsville, Tex., this week, the children generally have phone numbers of relatives in the United States written on their clothes or on slips of paper they carry in their pockets.

“These cases can be heartbreaking, because of how small the children are and because they are often very confused and scared by the entire ordeal,” said Lindsay Toczylowski, executive director of Immigrant Defenders Law Center in Los Angeles, which provides legal services to unaccompanied children.

How children end up on their own in the chaotic environment of the southwest border often follows a familiar pattern. Parents flee poverty and violence in countries like Honduras, Guatemala and El Salvador. They leave one or more of their children behind with relatives. Later, after settling in the United States, the parents send for the children they left behind, and those children make the journey with a relative or with strangers. After crossing the border, the children are often abandoned by smugglers and other migrants who believe the children will be rescued by the Border Patrol.

It is a tremendous gamble: Agents have, over the years, saved children’s lives in these situations.

One evening in June at the Arizona border, Border Patrol agents discovered a 6-year-old boy on a border road at a time when the temperature was more than 100 degrees. The abandoned boy was from Costa Rica, and told the agents that his uncle had dropped him off and had told him that the Border Patrol would pick him up. The boy said he was on his way to see his mother in the United States.

In July, agents in the Border Patrol’s Rio Grande Valley sector came upon an 8-year-old boy, alone, by a river road. Agents were only able to learn his name and his age as they took him in for processing — he spoke only a regional dialect they did not understand.

“We have gotten 4-year-olds, 3-year-olds that are abandoned by the smugglers and everybody else and kind of left to fend for themselves,” said Jorge Gonzalez, the patrol agent in charge of the Border Patrol’s Brownsville Station and a 19-year veteran of the agency.

One of the agencies that places children in foster homes said that a quarter of its caseload now consists of children 5 years old and younger.

Mr. Gonzalez and other officials said these unaccompanied children traveling without parents or relatives are sometimes even as young as infants and toddlers. In recent weeks, several infant boys and girls were being held at the Border Patrol’s Centralized Processing Center in McAllen, Tex. — all of them had crossed the border without their families, were apprehended as part of larger migrant groups and were expected to join relatives already living in the United States.

“We’ve seen that plenty of times,” Mr. Gonzalez said. “It’s a child that doesn’t belong to really, truly, anybody within the group, and they’re to get turned over to their parents that have already made their way into the United States.”

In one case, a 2-year-old girl was found with a group of migrants in November just north of the border near Campo, Calif. She was not related to anyone in the group, and was strapped to the chest of a 17-year-old boy in a makeshift cloth baby carrier.

The girl had been traveling with her mother, but the mother became tired and asked if one of the other migrants could carry her daughter. The 17-year-old boy agreed. But the group of migrants later separated, and the boy was unable to locate the girl’s mother. When he crossed into the United States with the girl still strapped to his chest, he had still not located the mother, according to the Border Patrol. After he and the girl were apprehended, the girl was placed in custody as officials worked on reuniting her with her mother.

In the case of the 3-year-old boy found on Tuesday in the cornfield, federal officials were working on reuniting the boy with his family. Pictures released on Twitter by the Border Patrol’s parent agency, Customs and Border Protection, show the boy sitting at a desk in a Border Patrol office, watching “Paw Patrol” on an official’s computer.

Children who arrive in the country alone pose a number of challenges to federal officials and to the agencies and contractors responsible for caring for them while they are detained. When children are too young to talk, basic communication is difficult. Many of these children can act out or withdraw, out of confusion and frustration with their situation.

“There are children 10 or younger who still make it alone,” said Anthony Enriquez, director of the unaccompanied minors program at Catholic Charities Community Services in New York, which represents more than 700 unaccompanied minors who are in the process of being deported. “In some cases, they make it in the company of an older sibling or in a group. We have run into kids who are so young they can’t express what they want. When you get into situations when you have a child who isn’t verbal yet and doesn’t have the capacity to comprehend the situation and make an informed decision, we have an ethical dilemma.”

These children illustrate the desperation of those coming to America. Many of these families who send for their children do not understand, or ignore, the dangers of the treacherous journey they are forcing the children to take. Boys and girls alike are at risk of being sexually exploited and abused by smugglers, of becoming seriously ill, or of dying from heat, cold or dehydration in the harsh, vast terrain on the southwest border. It is unknown how many cases of very young children traveling alone end in tragedy.

In 2014, a 12-year-old girl left Ecuador to reunite with her parents in the Bronx. She never made it. The girl — Noemi Álvarez Quillay — was sexually assaulted by smugglers at the border in Ciudad Juárez, Mexico. Days later, on March 11, 2014, still in Mexico, Noemi committed suicide by hanging herself from a shower curtain rod. A joint investigation that included United States law enforcement agencies led to the indictment in Mexico of more than 40 people involved in smuggling and assaulting Noemi and other women and children.

In Brownsville, Mr. Gonzalez recalled an incident about a year ago, when he worked at another South Texas station in rural Starr County. Agents discovered a boy who was 3 or 4 years old. He had a phone number for his aunt that he carried on a piece of paper.

“He was by one of the river landings, and he was actually caught with a group of aliens, but nobody said, ‘I brought him,’” Mr. Gonzalez said, adding, “Truthfully, there’s only one way he crossed, and that was with that group. But at that point, nobody wanted to take any kind of ownership of that situation.”

The agents contacted the boy’s aunt, and then the aunt put the boy’s mother in touch with the authorities. Both women were living in the United States.

“I think desperation is definitely part of it,” Mr. Gonzalez said. “I guess the situations that they currently reside in kind of dictate the manner in which they’ll try anything to get their family home again. I think that’s just the human condition. Everybody wants to be with their family, and they’re willing to do whatever it takes to do that.”

Manny Fernandez reported from McAllen, Tex., and Miriam Jordan from Los Angeles.

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