ILGA-Europe was founded in 1996, when its parent organisation, the International Lesbian, Gay, Bisexual, Trans and Intersex Association, established separate regions. It took over responsibility for supporting the development of the LGBT movement in Europe including Transgender Europe, Inter-LGBT, and for relationships with the European Union, Council of Europe and the Organisation for Security and Co-operation in Europe.
Initially ILGA-Europe worked entirely on the basis of volunteer resources. However, in 2001, its potential contribution to the European Union's anti-discrimination policies (established under Article 13 of the Treaty of Amsterdam) was recognised through the provision of core funding, currently through the PROGRESS Programme. This enabled ILGA-Europe to set up an office in Brussels, to recruit permanent staff, and to conduct an extensive programme of work in relation to sexual orientation discrimination within the EU Member States and the accession countries. Financial support from the Sigrid Rausing Trust, the Open Society Institute, Freedom House, the US State Department and the Ministry of Education, Culture and Science of the Netherlands allows ILGA-Europe to extend its work in areas not covered by EU funding, including Eastern Europe and Central Asia, and on transgender issues.
ILGA-Europe has hosted its annual conference at the end of October, since 2000, where member organisations elect the Executive Board and decide on the next year's working priorities.
- 2000 – Bucharest, Romania, theme Accepting Diversity
- 2001 – Rotterdam, Netherlands, theme Creating Partnership
- 2002 – Lisbon, Portugal, theme Recognising Diversity, Promoting Equality
- 2003 – Glasgow, United Kingdom, theme Policy into Practice – making LGBT equality happen
- 2004 – Budapest, Hungary, theme Coming out to the EU
- 2005 – Paris, France
- 2006 – Sofia, Bulgaria, theme We are Family – Our families in Europe and the European family
- 2007 – Vilnius, Lithuania, theme LGBT Rights are Human Rights – Respect, Recognition and Responsibilities
- 2008 – Vienna, Austria, theme Think globally, act locally
- 2009 – Malta, theme Overcoming Religious & Cultural Barriers to LGBT Equality
- 2010 – The Hague, Netherlands, theme Expressing our differences, challenging our prejudices, developing our alliances
- 2011 – Turin, Italy, theme Human Rights and "Traditional Values": clash or dialogue?
- 2012 – Dublin, Ireland, theme Advancing LGBTI equality in challenging economic times
- 2013 – Zagreb, Croatia, theme Family matters! Reaching out to hearts and minds
- 2014 – Rīga, Latvia, theme MOVEment: Leading Sustainable Change
- 2015 – Athens, Greece, theme Many voices, One movement - Together, mobilised for a just society
- 2016 - Nicosia, Cyprus, theme Power to the People - Celebrating 20 years of the strength within
- 2017 - Warsaw, Poland, theme Communities mobilising, Movements rising
- 2018 - Brussels, Belgium, theme From Words into Action
- 2019 - Prague, Czech Republic