Clarke also supports several charitable organisations. In September 2011, she joined the SMA UK Trust Team as their celebrity ambassador. The SMA Trust raises funds for research into spinal muscular atrophy. In August 2017, she became a patron of Open Door, a non-profit that aims to help young people gain access to drama school auditions. She auctioned a chance to watch an episode of Game of Thrones with her at the 2018 Sean Penn Charity Gala, which raised over $120,000 benefiting the J/P HRO & Disaster Relief Organizations. In February 2018, she introduced the award recipients at London’s Centrepoint Awards, which celebrates the courage shown by homeless young people.
In April 2018, she was named the sole ambassador to the Royal College of Nursing (RCN). As the RCN’s ambassador, Clarke pledged to use her voice to fight for greater investment in nursing and to challenge misconceptions. Clarke also pledged to join nurses and healthcare workers to tackle the issues affecting the profession, including a falling number in training and shortages in the current workforce.
Clarke was also one of the many UK based actresses to lend her voice to the Time’s Up movement which was aimed at exposing sexual harassment and abuse, and creating a society free of gender-based discrimination in the work place. In August 2018, Clarke, as well as Gemma Arterton, Lena Headey, Tom Hiddleston, Felicity Jones, Wunmi Mosaku, Florence Pugh, Gemma Chan, and Catherine Tate, featured in the short film titled Leading Lady Parts which took aim at the film industry’s issue of gender inequality during the casting process.
In 2019, following the announcement of the brain aneurysms she suffered in 2011 and 2013, Clarke launched her own charity SameYou. The charity aims to broaden neurorehabilitation access for young people after a brain injury or stroke. On 26 September 2019, she co-hosted a YouTube live stream with Irish YouTuber Jacksepticeye that raised over £200,000 for SameYou. After the conclusion of the final season of Game of Thrones a fundraiser called “Justice for Daenerys” was started in which fans of the show raised over £83,000 for her charity. According to the fundraiser creator, the purpose was to collectively show their appreciation for both Clarke and the character Daenerys Targaryen. In 2020, Clarke was presented with the Public Leadership in Neurology award by the American Brain Foundation for her efforts in raising awareness about neuro-rehabilitation.
In April 2020, Clarke started a fundraiser to help raise funds for her charity’s COVID-19 fund. The fundraiser, which aimed to raise £250,000, would support both the Spaulding Rehabilitation Hospital in Boston, Massachusetts, U.S. and the University College Hospital in London. The organizations new initiative aims to make a larger portion of beds available to coronavirus patients by providing a virtual rehabilitation clinic for people recovering from brain injuries and strokes. In a further response to the coronavirus pandemic, Clarke announced the launch of an Instagram series of poetry readings. The readings derive from a collection called The Poetry Pharmacy: Tried-and-True Prescriptions for the Heart, Mind and Soul. She began the series by reading a poem about loneliness, which she dedicated to her charity SameYou and announced that other performers would be joining the initiative, stating that every performer would dedicate their reading to a charity of their choosing.