On May 17, 1860, in Paris, in response to antisemitic incidents such as the abduction of Edgardo Mortara and the Damascus affair, he was one of the six founders of the Alliance Israélite Universelle.

"[3] Netter was appointed general secretary of the newly formed organization, and was joined 4 years later by French-Jewish politician Adolphe Crémieux who would serve as the president of the society while holding the position of French Minister of Justice.

During the first years Netter struggled with objections of the Jewish Old Yishuv leaders, who concentrated on Torah studies and relied on donations from Jews in the diaspora.

The Old Yishuv opposition to Jewish manual labor in the holy land, and clashes with Arab inhabitants of nearby Yazur disrupted development and recruitment of students.

He was involved in protecting the rights and safety of the Jewish community in Morocco, and was in charge of emigration of Russian-Jewish refugees to North-America following the introduction of the May Laws.

Charles Netter was one of the twenty signers of a petition sent to a Canadian Freemason leader, who subsequently agreed to the establishment of a lodge "in Jerusalem and surroundings".