Ilus' music career started at the age of four, when she began performing major roles in children's musicals across Estonia. Having gained a lot of performing experience at any early age, Ilus released her self-titled debut album Maarja in 1996, achieving reasonable success in her home country. Although the album made her known within her country, true national success would not come until the Eurolaul event later on that year. Ilus would perform two songs in the Eurolaul, "Kaelakee Hääl" and "Kummalisel Teel", the former a duet with Ivo Linna. The duet would ultimately win the competition, and she would go onto finish 5th in the Eurovision Song Contest 1996. The exposure from competing in Eurovision would ultimately make Geffen Records notice the young Ilus, signing her for her first international album release.
Meanwhile, Ilus entered the Eurolaul again in 1997, winning with the solo "Keelatud Maa". Ilus would eventually finish 8th in the Eurovision Song Contest 1997. The result helped to further solidify her popularity in Estonia, making her second album First In Line an instant success there when released on August 25, 1998. The album, which was Ilus' first effort entirely in English, was also released internationally, topping album charts in Japan and receiving considerable airplay in Germany, Sweden, Norway and Denmark. The success of the album made her, at the time, Estonia's most successful popular music artist ever. Ilus would not achieve the same success when she tried to break through into the American mainstream, though, with the album essentially failing to make any impact on the Billboard charts. Ilus would also release the mostly Estonian language album Kaua Veel later on in 1998, with the album winning her the Estonian Female Singer of the Year award. In 1999 she also became a Goodwill Ambassador for UNICEF.
Ilus' next album would be City Life in 2001, which again achieved reasonable success in Estonia. The album would not, however, repeat the international success of First In Line. Following the release of City Life, Ilus' international popularity faded a little, although she still remained a notable celebrity in Estonia. Ilus would enter the Melodifestivalen of 2003 in Sweden with the song "He is Always On My Mind", although she would be eliminated at the semi-final stage. The appearance in Melodifestivalen helped to re-establish Ilus in Sweden a little, but the release of the song as a single (and release of a modified version of City Life, with the song as the first track) was a commercial failure.
Ilus would enter Eurolaul for the third time in 2004, performing the self-written "Homme", but she would ultimately finish in 4th place. Since 2004 Ilus has worked on smooth jazz projects, working with the club jazz band Hinkus and performing vocals on Tõnu Raadik's Flow of Dreams album. She also recorded a duet with the Latvian pop singer Lauris Reiniks in 2005, with the song becoming a hit in both Estonia and Latvia.
In early 2006 Ilus publicly stated that she was unhappy that former Vanilla Ninja bassist and lead vocalist Maarja Kivi, another Estonian singer who has achieved international success, was also using the performing name of Maarja for her debut solo single. The two using the same name has confused some into believing that Kivi and Ilus are the same person.