The role has traditionally rotated with the association's presidency, but the organisation has decided to make the job permanent. Brown will become the first to hold the position when the presidency next rotates in July.
"I'm delighted to take the role and I will be working closely with the president on agendas, activities and information sharing," he said.
"There are a number of areas we will be looking at in the future, not least the sustainable use of pesticides directive."
Brown pointed out that there was a need for a greater exchange of views across Europe to ensure that the implementation of the directive was consistent across the continent.
As permanent secretary, Brown will help cement British influence on the group, currently under the leadership of Belgian grower Willy De Nolf. Spanish member Jaume Rierais will become president in July.
Another area likely to dominate the ENA's agenda following Brown's appointment will be the reform of plant health. The European Commission consulted the group last December in preparation for upcoming reforms.
Initial findings are expected to be released in the summer and Brown said he was confident that they would be "sensible."
He added: "We would like to see closer links between the inspectors in different countries. There are good links between the policy people but not such good ones for the inspectors and that needs to be strengthened."
Better communication between plant health inspectors is said to be needed in the light of the longhorn beetle outbreak in Boskoop, though Brown denied the incident would have a significant effect on the consultation.
De Nolf welcomed Brown's appointment. "It will make things easier to have someone permanent in the position and for some countries it has always been difficult to fill the secretariat," he said.