The inaugural event, called the Mad-Croc Rally Estonia for sponsorship reasons, was held in 2010 as part of the Estonian Rally Championship. It was won by Markko Märtin and Kristo Kraag, who swept all special stages. Mads Østberg and Jonas Andersson became the first two-time winners by claiming back-to-back victories in 2011 and 2012 in a Ford Fiesta RS WRC. Georg Gross and Raigo Mõlder took local honours in 2013 in a Ford Focus RS WRC.
From 2014, Rally Estonia joined the FIA European Rally Championship. That first ERC season saw Ott Tänak and Raigo Mõlder win in a Ford Fiesta R5, and the event was named ERC Rally of the Year. The 2015 edition produced a notable upset when Aleksey Lukyanuk and Alexey Arnautov won overall in a lower-specification Mitsubishi Lancer Evo X, beating the more powerful R5 field. In 2016, Lukyanuk and Arnautov were leading again until crashing out on the penultimate stage, handing victory to Ralfs Sirmacis and Māris Kulšs in a Škoda Fabia R5.
After a hiatus in 2017, the rally returned in 2018 under the Shell Helix Rally Estonia banner. It became a popular pre-season test venue for WRC works teams preparing for Rally Finland. The 2018 edition was the first competitive outing for the new Toyota Yaris WRC outside the WRC series. Ott Tänak and Martin Järveoja dominated, winning eleven of sixteen stages. In 2019, Rally Estonia became the first-ever official WRC Promotional Event, with every WRC manufacturer team entering. Tänak and Järveoja again won convincingly, losing only two stages. The event attracted more than 52,000 fans, a twenty-five percent increase on the previous year, and registered more than 25 million social media impressions.
Rally Estonia was added to the 2020 WRC calendar after the COVID-19 pandemic forced the championship to seek replacement venues. Held in September 2020, it marked the championship's return after a six-month halt and was the 600th event since the WRC was founded in 1973. Tänak and Järveoja won for Hyundai on home soil, completing a Hyundai one-two with Craig Breen and Paul Nagle second. The event received widespread praise and was awarded the WRC Team Spirit Award for executing a COVID-safe maiden WRC event within sixty-three days.
Rally Estonia was included on the 2021 calendar as round seven. Tänak suffered double punctures in consecutive stages early in the rally, ending his home hopes. Kalle Rovanperä and Jonne Halttunen claimed victory, with Rovanperä becoming the youngest WRC winner in history at twenty years and 290 days, breaking the previous record held by Jari-Matti Latvala.
The 2022 edition served as the first high-speed gravel test for WRC's new hybrid Rally1 cars. Rovanperä again dominated, winning fourteen of twenty-four stages, finishing more than a minute ahead of Toyota team-mate Elfyn Evans. In 2023, Rovanperä and Halttunen secured a third consecutive Rally Estonia win, sweeping fifteen of twenty-one stages over the final two days in a display reminiscent of Sébastien Loeb's stage-win streak at the 2005 Tour de Corse.
When Rally Latvia was added to the 2024 WRC calendar, Rally Estonia dropped off and returned to the ERC. In 2025, Rally Estonia came back to the WRC. Oliver Solberg led from Friday and held off Tänak and Thierry Neuville to claim his maiden WRC victory.
Rally Estonia has accumulated multiple accolades, including the 2014 ERC Rally of the Year, the 2020 WRC Team Spirit Award, and FIA's three-star environmental accreditation in 2022. Its smooth, fast gravel roads and enthusiastic crowds have made it a favourite among drivers and teams, and it is consistently cited as one of the better-organised events on the WRC calendar.