As a youth, Carneiro played the viola. In Portugal, Carneiro studied music at the Academia Nacional Superior de Orquestra in Lisbon, where she attended the class of Jean-Marc Burfin. She earned a master's degree in music at Northwestern University, studying with Victor Yampolsky and Mallory Thompson. She continued graduate studies in music for a doctorate at the University of Michigan, where her teachers included Kenneth Kieser. At the University of Michigan, she also served as the conductor of the University Symphony Orchestra and University Philharmonia Orchestra.
Carneiro first gained attention as a finalist in the 2002 Maazel-Vilar Conductor's Competition at Carnegie Hall. She then served as Music Director of the Los Angeles Debut Orchestra from 2002 to 2005. She has worked as an assistant conductor with the Los Angeles Chamber Orchestra. She was an American Symphony Orchestra League Conducting Fellow with the Los Angeles Philharmonic from 2005 to 2008. In Portugal, Carneiro became Principal Guest Conductor of the Metropolitan Orchestra of Lisbon as of the 2005–2006 season. In the 2006–2007 season, she became principal guest conductor of the Gulbenkian Orchestra, and held the post through the 2012–2013 season.
In the US, in January 2009, Carneiro was named the third music director of the Berkeley Symphony, effective with the 2009–2010 season, with an initial contract of 3 years. The first woman to hold this post, the position marks Carneiro's first music directorship, and her first concert in that capacity took place in October 2009. In May 2018, the Berkeley Symphony announced the conclusion of Carneiro's music directorship of the orchestra at the end of the 2017–2018 season, at which time she is to take the title of music director emerita.
Carneiro will make her Edinburgh International Festival debut in August 2019, leading the BBC Scottish Symphony Orchestra and organist Stephen Farr in a performance of Sir James MacMillan's pieces A Scotch Bestiary and Woman of the Apocalypse. 
Carneiro has been married twice. Her first husband was Simão Vital, an investment banker. Her second marriage, in September 2011, was to José de Assunção Gonçalves, a physician. The couple are the parents of triplets, born in February 2017.
- 2002: National Conductor Search of the Young Musician's Foundation
- 2010: Helen M. Thompson award from the League of American Orchestras
- Ralph Blumenthal (2002-09-30). "And Then There Were Two; Prize Is Shared in Conductors' Competition". New York Times. Retrieved 2011-02-13.
- Joshua Kosman (2009-01-16). "Joana Carneiro to conduct Berkeley Symphony". San Francisco Chronicle. Retrieved 2011-02-13.
- Joshua Kosman (2009-10-17). "Fine start at Berkeley Symphony". San Francisco Chronicle. Retrieved 2011-02-13.
- "Joana Carneiro announces her intent to step down as Music Director of Berkeley Symphony after nine seasons" (PDF) (Press release). Berkeley Symphony. 24 May 2018. Retrieved 2018-05-26.
- Vanessa Alto (2013-09-20). "Pinamonti volta ao São Carlos sete anos após saída polémica". Publico. Retrieved 2013-11-17.
- "BBC Scottish Symphony Orchestra". Edinburgh International Festival. 2019-05-21. Retrieved 2019-05-22.
- Ana Sofia Coelho (2017-02-09). "Maestrina Joana Carneiro foi mae de trigemeos". Move Notícias. Retrieved 2017-08-02.
- Georgia Rowe (2017-05-12). "Berkeley Symphony announces new season; Joana Carneiro returns to conduct". San Jose Mercury News. Retrieved 2017-08-02.
- "Maestrina Joana Carneiro distinguida com prémio nos EUA". Publico. 2010-06-19. Archived from the original on 2012-03-29. Retrieved 2011-02-13.
- IMG Artists agency biography of Carneiro
- Los Angeles Philharmonic Orchestra biography of Carneiro
- Berkeley Symphony biography of Carneiro
- Gulbenkian Orchestra Portuguese-language biography of Carneiro
- Michael Zweibach, "Joana Carneiro: Enjoying Her Breakout Year". San Francisco Classical Voice, 1 December 2009