The first Alternative Songs chart appeared in the September 10, 1988 edition of Billboard magazine, then known as "Modern Rock Tracks". The first song to reach the chart's No. 1 position was Siouxsie and the Banshees' "Peek-a-Boo", which topped the charts for two weeks. In the chart's early years, the chart was closely associated with college rock, new wave, post-punk and electronic genres with a large presence of British, Irish and Australian artists, as only 24 of the chart's first 82 number-one hits were by American acts. Bands including Depeche Mode, Pixies, The Cure, New Order and R.E.M. were amongst the most popular acts on Alternative radio in the late 1980s and early 1990s. Many rock artists do not release commercial singles in the United States. Several popular songs which were not released as commercial singles did not qualify for the Hot 100 before December 1998, but performed very well on the Modern Rock Tracks chart.
In 1991, with the release of "Smells Like Teen Spirit" by Nirvana (which reached No. 1 on November 23, 1991), grunge became a new form of alternative rock to chart. However, grunge did not have a dominating presence on the chart in its heyday; over time, grunge would grow into popularity as a representation of alternative rock in the mainstream. Iconic grunge songs fared decently on the Alternative Songs chart but better on the Mainstream Rock Songs. For example, "Black" by Pearl Jam peaked only at No. 20 on the former but No. 3 on the latter. This was because the college rock and new wave of the 1980s remained the dominant styles of the format, while grunge became an alternative rock style that was popular on the Mainstream Rock format.
In the mid-1990s, alternative rock songs began to crossover to Pop radio, with acts such as Green Day, The Offspring and Alanis Morissette being played on Pop stations after establishing hits on the Alternative chart. Dominant genres included pop punk and softer alternative rock, as grunge acts such as Soundgarden and Stone Temple Pilots did not reach No. 1, while Britpop, a form of alternative rock from the UK, was represented only by Oasis. By the late 1990s, the Alternative Songs chart was ruled by relatively lighter alternative rock bands such as Third Eye Blind, Matchbox Twenty and Sugar Ray and a plethora of one-hit wonders.
At the turn of the century, alternative radio embraced nu-metal/rap rock with bands including Korn, Limp Bizkit and most famously, Linkin Park. Chris Molanphy of Pitchfork stated that "possibly the most loathed period for music of the last half-century, the rap-rock years-- when looked through the prism of the Modern Rock chart’s evolution-- are a logical endpoint to a decade when alt-culture steadily de-wussified itself." Garage rock from the likes of The White Stripes and The Strokes also became hits in the early 2000s as a counter to the over-aggression of rap rock.
In the mid-2000s, the Alternative charts were ruled at the top by its most dominant members. From 2003 to 2008, the No. 1 song was by either Foo Fighters, Green Day, Incubus, Linkin Park or Red Hot Chili Peppers 49% of the time – 152 out of 313 weeks. During this time, classic '90s alternative groups such as Nine Inch Nails and Weezer enjoyed their biggest success, while emo (Jimmy Eat World), indie rock (Modest Mouse) and pop punk (Fall Out Boy) also were popular. In 2007, "The Kill" by Thirty Seconds to Mars set a record for the longest-running hit in the history of the US alternative chart when it remained on the national chart for 52 weeks. Rise Against's "Savior" later broke the record by spending 65 weeks, followed around the same time by "1901" from Phoenix at 57. In 2009, Billboard renamed the chart to "Alternative Songs".
In the 2010s, the Alternative charts were led by softer indie pop and folk, and crossed over new acts to pop radio for the first time since the late '90s; these acts being Foster the People, Imagine Dragons, fun., and Gotye. The chart also began to diverge from the Mainstream Rock chart, as only 10 of 40 songs were shared between the two in November 2012, compared to 23 of 40 in November 2002. For the chart's 25th anniversary in 2013, Billboard published a list of the 100 biggest hits in the history of the Alternative chart. "Uprising" by Muse was listed at No. 1, having spent 17 weeks on the top of the chart and 53 weeks in total. "Savior" by Rise Against was listed at No. 2, peaking at #3 but staying on the chart for a record-breaking 65 weeks.
In 2018, Billboard released its Greatest of All Time Alternative Songs 30th-anniversary recap. The Foo Fighters continued its reign as the chart's No. 1 act over the list's first 30 years, after leading the 25th-anniversary recap. Muse's "Uprising" retained its standing as the all-time No. 1 song. Rise Against's " Savior" again ranked at No. 2, while Portugal. The Man's "Feel It Still" entered at No. 3, the highest debut on the 30th anniversary songs list, following its record 20-week reign in 2017. Only six bands have charted in all four decades of the chart's existence – Nine Inch Nails, Depeche Mode, Jane's Addiction, Red Hot Chili Peppers, U2 and Beastie Boys.