In December 1988, Lothian Regional Council (LRC) and Lothian Health Board (LHB) announced the formation of a new body, the Waverley Care Trust. Responsibility for the organisation of Trust meetings rested with the Regional Secretary’s Department and trustees included the Lord Provost of the City of Edinburgh, the Chairman of Lothian Health Board and the Bishop of Edinburgh. Waverley Care Trust, working with the Milestone Venture Trust, was responsible for the establishment of a residential care facility for people with HIV and AIDS called Milestone House, which opened in 1991 in the grounds of the City Hospital.

In 1993, the SOLAS Information and Resource Centre, which had previously been run as an independent organisation, became a sister project of Milestone House, offering a community space for those affected by HIV to obtain information and support. In the following years, the Waverley Care Arts Project was jointly administered by SOLAS and Milestone, with art-based activities being delivered in both locations. Another key function was added in 1996, with the establishment of the Buddy Service, which offered the opportunity for those affected by HIV and AIDS to receive one-on-one support from trained volunteers.

In July 2003, the organisation was incorporated as a Company limited by guarantee under the name Waverley Care. Waverley Care's organisational remit expanded to include all blood-borne viruses, formally acknowledging the increased work Waverley Care was doing with those diagnosed with Hepatitis C. Geographically, the charity also broadened its scope in the 2000s: 2005 saw the African Health Project being delivered in Glasgow from a new office in the city, while in 2007, the first national project was launched in the form of an outreach and support initiative for children across Scotland affected by HIV. The work of Waverley Care was extended to Lanarkshire, Fife and the Borders in 2009, and then to the Highland area and Argyll and Bute the following year, with a new office being opened in Inverness.