The 'Harry Potter' author had been criticised by some of her fans for not joining the boycott alongside other people from the creative industries in response to the continuing conflict in the Middle East.
Her decision to co-sign a letter which directly countered one written by artists, authors and actors in support of a cultural boycott led to claims that Rowling was herself a 'Zionist' supporter of Israel.
In the letter, published last week, the signatories talk about their disagreement with the boycott of academia, art and literature as part of the wider boycotts, divestment and sanctions movement - known as BDS (Boycott, Divestment and Sanctions movement).
The signatories wrote: "Cultural boycotts singling out Israel are divisive and discriminatory, and will not further peace."
A previous letter had presented support for a cultural boycott from prominent figures in the arts and academia.
Tensions between Israel and Palestine appear to have heightened in recent weeks after a steady spate of knife attacks across Israel's Arab cities have led to fears of a possible third intifada.
The peace process has almost entirely broken down, with Israel's far-right government, led by Benjamin Netanyahu, emboldened by an increased majority at the last election.
In a post on Twitter, Rowling defended her decision by saying that a cultural boycott has not solved any violent conflicts in the past and that it is unlikely to do so in the middle east.
She wrote: "Speaking purely for myself, I have deplored most of Mr Netanyahu's actions in office. However, I do not believe that a cultural boycott will force Mr Netanyahu from power, nor have I ever heard of a cultural boycott ending a bloody and prolonged conflict.
"If any effects are felt from the proposed boycott, it will be by ordinary Israelis, many of whom did not vote for Mr Netanyahu.
"The sharing of art and literature across borders constitutes an immense power for good in this world."
What is BDS?