In the 1990s Vaiksoo toured Europe with the Eesti Televisioon (ETV) concert choir. In 2000 she received fourth place at the all-Estonian song contest for children, organized by ETV. Vaiksoo's first stage performance in a musical was the 1998 Estonian original production of The King and I where she performed as a choir artist.
- 1998: The King and I (choir artist) Tallinn City Hall
- 2000: Tanz der Vampire (Sarah) Tallinn City Hall
- 2001: No, No, Nanette (choir artist) Tallinn City Hall
- 2001: Les Misérables (Cosette, understudy) Tallinn City Hall
- 2002: Miss Saigon (Kim) Tallinn City Hall
- 2003: Aida (Amneris, understudy) Theatre Vanemuine
- 2003: Miss Saigon (Kim, understudy) Germany, Luxembourg
- 2003: Oliver! (Bet) Tallinn City Hall
- 2004: Crazy for You (choir artist)
- 2005: West Side Story (Maria) Theatre Vanemuine
- 2005: Cats (Jemima) Theatre Vanemuine
- 2005: Cinderella (Cinderella) Tallinn City Hall
- 2006: Fame (Serena) Tallinn City Hall
- 2007: Personals (Claire)
- 2007: Phantom (mother) Tallinn City Hall
- 2007: Pippi Longstocking (Pippi) Tallinn City Hall
- 2008: Tanz der Vampire (Sarah) Oberhausen, Germany
- 2011: Pippi Longstocking (Pippi) Estonian National Opera
- 2011: Mary Poppins (Mary Poppins) Theatre Vanemuine
- 2012: Dreams From A Summer House (Belle)
- 2013: Shrek (Fiona)
Nele-Liis Vaiksoo has given her voice to the Estonian version of Disney`s Tangled (2011) by dubbing the leading character´s voice, the one of Rapunzel. At 2012, she gave her voice to another Disney`s 3D animation The Lion King by dubbing the voice of Nala.
In 2003 the album We Are Family was released, which was recorded by Vaiksoo and eight other Estonian solo artists, such as Kaire Vilgats, Maiken, Bert Pringi, Lauri Liiv, and Lauri Pihlap. In 2008 she released a Christmas album together with Rolf Roosalu.
In 2011, Nele-Liis Vaiksoo released a concept album of the musical "Pipi Pikksukk" ("Pippi Longstocking") in which she played the lead character, Pipi. In 2013, she released an album "Mina" ("Me") to celebrate her 15 years on musical stage. The album consists of numbers from different musicals in which she has or still hopes to play in ("Les Miserables", "Little Shop of Horrors", "Cats", "Cabaret", "Chess" and many more).
- "Nele-Liis Vaiksoo: "Olen leidnud inimese, kellega tahan koos olla"" (in Estonian). Naistemaailm. Retrieved 11 July 2008.
- "Rolf Roosalu ja Nele-Liis Vaiksoo annavad välja jõulualbumi ..." (in Estonian). elu24.ee. 13 November 2008. Retrieved 7 June 2010.
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