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The club was founded in 1960 as Estelí FC, adding Real to its name in 1961. Estelí FC plays at the Estadio Independencia, one of the biggest stadiums in Nicaragua, with a capacity of 4,800. The club is known by the nickname, El Tren del Norte (Train of the North), coming as it does, from the northern region of Las Segovias.

Real Estelí has finished in the top five of Nicaragua's top flight every year since 1986. In that time, they have also achieved traditionally high attendance numbers. However, it took time for the club's burgeoning popularity to translate into championships.

The club under Leonidas "Cascarilla" Rodriguez and Honduran Roy Posas were able to win the club first silverware, winning both the League and cup double. Players that contributed with players such as Otoniel Olivas, Salvadoran Julio "El Cura" Barahona, Honduran Samuel Nunez, and Ramon "ElChino" Mejia then added another in 1999. Nonetheless, their fierce rivals Diriangén FC remained the dominant power in Nicaraguan football.

This began to change in 2002–2003. The two clubs met for a two-legged tie to determine the year's champion. Diriangén won the first leg 1–0, but Real Estelí answered by winning the return match 3–0, claiming the title 3–1 on aggregate. That was the last year Nicaragua determined their championship with a "long season"; for 2003–2004, the league adopted an Apertura/Clausura format. Real Estelí won both tournaments, and each time they defeated Diriangén in the finals.

The following September, Real Estelí made history in Nicaraguan football by eliminating favorites Real España in the First Round of the Copa Interclubes UNCAF. They thus became the first Nicaraguan football team in history to advance to the second round of the tournament.

Back home, Diriangén won the next two championships, but quickly gave way to Real Estelí, who embarked on their dominant run of eight championships in a row from 2006 to 2014. Then, after a brief interruption by Walter Ferretti, Estelí won two more.

Real Estelí FC has finished in the top five of Nicaragua's top division every year since 1986 and has achieved some of the highest attendances in the league during this period.

In 2023 CONCACAF Central American Cup, Making their first appearance in the modified Tournament, Real Esteli finished second in group, where they defeated highly rated opponents FAS, Xelaju and Olimpia, The club only loss was against Independiente who toped the group. In the Quarter Final, Real Estelí Made history by winning their two legs series against Concacaf heavyweight Saprissa 3-2. Not only becoming the first Nicaraguan club to defeat Saprissa but also the first Nicaraguan to qualify to the semi final of an international tournament. In the semi-finals against Independiente they defeated the Panamanian side 3-2 in two legs to advance to the first international final in the club's history. However, in the final played over two legs, Costa Rican Giants Alajuelense would beat Real Esteli 4–1.

Real Esteli entered the 2024 CONCACAF Champions Cup in the first-round and faced off against seven-time champions Club America. Esteli won the home leg 2–1, which marked the club's first win in the competition in 31 matches.

Crest

The club crest consists of a crown, representing 'Real' (meaning 'Royal'). Similar crowns can be seen on the crests of many other clubs with the prefix 'Real', such as Spanish clubs Real Betis, Real Zaragoza and Real Madrid

The two gold stars of the crest mark the first two national championships won by the club (in 1991 and 1999), while the red and white striped shield represents the club colours as used on team shirts. The logo was redesigned and digitalised in 2000 by Nakor'd J. García and Michael D. Raney (current President/CEO of the World Football Organization), based on the original design by Arnulfo Rivera Zeledón and Johnny Herrera Vallejos.

'El Clásico' rivalry

There is often a fierce rivalry between the two strongest teams in the national league, where the game between Real Estelí and Diriangén has become known as El Clásico (The Classic).