Alexis Deswaef, FIDH's vice president, was picked up by officers at his hotel on Monday after two days in the country, taken to the airport and put on a flight to neighboring Ethiopia, the group said in a statement.
The police officers, who also confiscated Deswaef's notebooks, mobile phone and SIM cards, gave no reason for the expulsion, it said.
During his two days in the country, Deswaef met with human rights representatives, unions, opposition politicians, foreign diplomats and United Nations staff.
While in Djibouti, Deswaef was followed by a man in military uniform and another in plain clothes in an unmarked car, FIDH said.
"Djibouti pays little attention to human rights and is sliding towards authoritarianism," Deswaef was quoted as saying in the statement.
"Why would they fear an NGO mission and what are they hiding?"
The visit came after the ruling party in Djibouti last month retained its significant majority in parliament following elections it was assured of winning after an opposition boycott.
On Sunday, a program director on the same mission for the FIDH and also in possession of a visa, was refused entry at Djibouti airport and put on a flight to Istanbul, with police also refusing to give "the slightest reason" for prohibiting her entry, it said.
The main opposition parties in the tightly controlled Horn of Africa nation refused to participate in the legislative vote, denouncing the process to elect 65 MPs as a sham.
President Ismail Omar Guelleh, who has ruled the country since 1999, was re-elected for a fifth term with 97 percent of the vote in 2021.
His rule has seen a crackdown on press freedom and dissent.
Despite its small size, Djibouti enjoys a strategically crucial position at the mouth of the Red Sea, which it uses to woo trade investors and foreign military powers.
Several major nations have military bases in the country, including France, the US, Britain, Germany and China.
"What happened to my colleagues is unacceptable, but not surprising," FIDH President Alice Mogwe said in the statement.
"What is more surprising is the passivity of European governments, the United States and China, who are happy to use their bases in Djibouti without caring about what is happening to the local population."