Pekanovic announced his decision during a debate on his replacement which had been requested by a group of councillors dissatisfied with the way Pekanovic pushed for the Croatian community's interests and the way the HNV's money was being spent.
The new president is expected to be elected at a session next week.
The chair of the HNV Executive Committee, Slavica Peic, said the resignation would not obstruct the Council's work.
Also today, councillors gave their consent to the proposed appointment of Jasminka Dulic as new editor of Hrvatska Rijec, the only Croatian news weekly in Serbia.
The HNV was established in 2002 to represent the Croatian minority's interests in the use of their official language, education, information and culture.