Phoenix has held academic posts as Lecturer in Criminology at the University of Middlesex from 1998 to 2000, the University of Bath until 2000 and a variety of posts at the University of Durham until 2013 (reader in criminology, made professor in 2010, deputy head of the Faculty of Social Sciences and Health, Dean of Queens Campus) and Head of the law department at the University of Leicester.^[6] She was Professor of Criminology at the Open University, before moving to University of Reading. Phoenix is a trustee of the Centre for Crime and Justice Studies.^[6]

Her research areas include sex, gender, sexualities, prostitution policy and the experience of women in prison. She has written two books, Making Sense of Prostitution ^[7] and Illegal and Illicit: Sex, Regulation and Social Control (with Sarah Oerton). Phoenix edited Regulating Sex for Sale^[8] and several articles and book chapters on the sex industry ^{[9] [10] [11] [8] [12] [13]} and experiences of supporting transgender persons in the prison estate. ^[14]

Reviewers of her books describe "the paradox that cannot have escaped the attention of many readers in the field: that the apparent increase in freedom, choice, and diversity in sexual matters is conversely and simultaneously matched by a 'proliferation of laws, policies and guidelines which seek to determine the complex, vast and ever-increasing rules of engagement'".^[15] Phoenix gave evidence to the UK Parliament regarding the multiple disadvantages that women experience in the criminal justice system, particularly working class women and women of colour. In relation to community-based punishments and services, she lobbied for continued provision of women-only, single sex spaces for women.^[16]

Phoenix is one of the two academic speakers (along with Rosa Freedman) who received an apology from the University of Essex in 2021 after their invitation to speak about transgender rights in prisons was withdrawn at short notice due to students claiming that Phoenix is transphobic.^[17][18][19] In November 2021, Phoenix welcomed legal action against the University of Essex, claiming its policies breach free speech legislation. The Free Speech Union, led by Toby Young, took the action.^[20] An investigation found the decision to withdraw the invitation "amounted to a breach of Prof Phoenix's right to freedom of expression".^[21]

In 2021, Phoenix began a process of bringing a constructive dismissal case against the Open University (her employer) for not protecting her against harassment in the workplace.^[22] She has stated that she hopes the "case will help to establish a line in the sand and make it clear that baseless accusations of transphobia simply for standing up for the rights of women is harassment especially when made in an academic context". She left the Open University to take up a professorial role in the law school at the University of Reading.^[23][24] In January 2024, the Tribunal found in her favour. The judgment said that she had been constructively unfairly dismissed, and that she had suffered victimisation, harassment (which included being compared to a "racist uncle"), and direct discrimination by the Open University, which did not allow her to speak about her negative treatment in department meetings due to her research, and failed to protect her from deplatform campaigns and being called a "transphobe" or "TERF" on social media.^[22] In March 2024, Professor Phoenix announced that she had agreed a compensation settlement with the Open University. The amount to be paid was not disclosed.^[25]

In June 2021, Phoenix and Jon Pike (a researcher in philosophy of sport)^[26] convened the Gender Critical Research Network (GCRN) at the Open University.^[27] The network aims to "bring together a range of academics and scholars, all of which share a common interest in exploring how sexed bodies come to matter in their respective research fields and a common commitment to ensuring that a space within academia is kept open for those explorations".^[28] Philosopher Kathleen Stock and Historian Selina Todd are members.^[28]

The network was criticised and described as transphobic in an open letter signed by 368 people, which called on the Open University to withhold support and funding.^[4][29] The letter said the network was "hostile to the rights of trans people" and said that academic freedom should not be "at the expense of marginalised groups".^[1] Phoenix has stated formally that she supports "the rights of trans individuals to be fully protected by the Equalities Act and welcome government reform of the Gender Recognition Act in ways that are sympathetic to their needs" but proposes that an individual’s right to identify as a particular gender should not be the basis upon which provision of criminal justice is based.^[16] The open letter was cited by the employment tribunal as one of the instances of harassment against Phoenix by her colleagues.^[22]

In November 2021, the Open University's vice-chancellor's executive stated that "the formation of the GCRN was compatible with academic freedom, while also acknowledging that some staff found the content of the group's work to be challenging or concerning" and undertook to review of its own policies and procedures.^[30] In an apology issued following the 2024 tribunal ruling, Professor Tim Blackman, Vice-Chancellor of The Open University, stated that "The University has supported and continues to support the work of the Gender Critical Research Network (GCRN) as part of the many important research activities that take place at the OU", and "The tribunal ruling makes it clear that we should have acted differently to address the impact of this reaction on Professor Phoenix and the working environment that she experienced."^[5]

Phoenix has Ehlers-Danlos syndrome. She and her partner, a glass artist, have been together since 2005.^[31]