Sisi was accorded an official reception, where the national anthems of the two countries were played.
Later on, the two presidents held a session of talks at Bellevue Palace, said Egypt's Presidential Spokesman Alaa Youssef.
The German president welcomed Sisi and affirmed that his visit to Berlin is historic, said the spokesman.
He also said that his country waited for this visit to get acquainted with Egypt's viewpoints toward several issues, according to the spokesman.
Gauck also hailed Egypt's regional role in the Middle East and voiced his country's desire to become Egypt's partnership in supporting security and stability in the region along with combating violence.
Sisi, for his part, voiced happiness for visiting Berlin for the first time, noting that the German experiment is a model worthy of respect and study, said the spokesman
Sisi also hailed the German people for their devotion to work, he added.
Gauck said that his country appreciates the enormity of task undertaken by Sisi to attain economic progress and meet people's needs.
The two sides also exchanged viewpoints regarding the latest death sentences in Egypt.
Sisi affirmed his respect for the Egyptian judiciary and said that he did not interfere or comment on any judicial ruling.
The referral of the rulings to the mufti is only advisory and "has no relation whatsoever to the death sentence," he said.
"The death sentences are mostly issued in absentia, and are then overturned once defendants turn themselves in; then retrials begin pursuant to both Egyptian and international laws," he went on to say.
"These are not exceptional or revolutionary courts", he said.
On the sentences, Sisi said that this is the first step of litigation and all death sentences are challenged by Egypt's prosecution before going into the next step of litigation.
The German president thanked Sisi for this clarification and called for holding dialogue between the legal experts of the two countries to exchange viewpoints on the judicial systems in the two countries.
Sisi also affirmed that some youths were arrested for destroying public and private property and committing crimes under the cover of protests.
The protest law does not ban staging demonstrations but it regulates it to provide the climate conducive to tourism and investment, he added.
The spokesman, meanwhile, said that Sisi underlined Egypt's role in renewing the religious discourse.
He also pointed out to Al Azhar's role in this respect to disseminate the values of tolerance.
Sisi also affirmed that the current stage witnesses the establishment of a modern and democratic state in Egypt.
Egypt appreciates the citizenship value and does not discriminate between its citizens, he added.
The German president said that there are several aspects of cooperation between the two countries that could be promoted, topped by energy and vocational training, he added.
The meeting also tackled the latest regional conditions, especially efforts related to pushing forward peace talks between Palestinians and Israelis along with the crisis in Libya.