Eskandar is the first Copt to assume the prestigious post.
The NCHR said the presidential decree is testament to President Abdel-Fattah El-Sisi's "insightful vision and his human rights approach."
"It adds a giant step in the field of civil and political rights to the previous important steps to assure that each Egyptian is afforded their full rights without any discrimination and also reflects the president's determination to implement the newly issued National Strategy for Human Rights," said Moushira Khattab, the NCHR president.
"Egypt is ushering in a new era in which the political leadership holds in high value the civil rights and the principle of equal opportunities for all citizens without any discrimination based on religion, gender, or any other reason," Khattab added.
The appointment of Eskandar proves that competence alone is the criterion for promotion, noted the president of the NCHR.
As per El-Sisi's decree, Eskandar, 65, will take over the SCC's presidency from Said Maree Mohamed Gad starting Wednesday, according to the official gazette.
Eskandar served as the vice president of the SCC in 2010 and then as president of the Cairo Appeal Court until he was reappointed as the vice president of the SCC in 2014.
The president has the authority to choose the head of the SCC from the five longest-serving deputy chairs for a one-time term of four years, which ends if the age of retirement, 70, is reached.
The SCC is the country’s autonomous and independent judicial authority in charge of ensuring that the domestic laws and regulations are in line with the constitution.