He was born in 700 A.D. Madina. He was the son of Muhammad bin Ali, also known as Muhammad al-Baqir and the grandson of Ali ibn Hussain (also known as Zainul Abideen). This made him a direct decendant of the Prophet of Islam - Muhammad (through Ali Ibn Abi Talib and Fatima Zahra and their son Hussain ibn Ali . His mother Umm-e-Farwah was the great grandaughter of Abu Bakkar (The First Caliph of the early Islamic State).

As a child, Jafar studied under his grandfather, Zainul Abideen. After his grandfather's death, he studied under and accompanied his father, Muhammad al-Baqir . Jafar's father would die in 743 (A.D). As the son of two prominent Imams, and descendents of Muhammad, he would become well versed in Islamic sciences including Hadith, Sunnah , and the Quran.

Imam Jafar was famed for his depth and breadth of knowldege. In addition to his knowledge of Islamic sciences, Imam Jafar was well educated in natural sciences, mathematics, philosophy , astronomy , anatomy , chemistry (alchemy), and other subjects. The foremost Islamic alchemist Jabir bin Hayyan (known in Europe as Geber) was his most prominent student. Other famous students of his were Imam Abu Hanifa and Imam Malik Ibn Anas, the founders of two Sunni schools of jurisprudence, and Wasil ibn Ata, the founder of the Mutazilite school of Islamic thought. Imam Jafar was known for his liberal views on learning, and was keen to debate with scholars of different faiths and of different beliefs. Imam Abu Hanifa is quoted by many souces as having said "My knowledge extends to only two years. The two I spent with Imam Jafar Sadiq", some Islamic scholars have gone so far as to call Imam Jafar Saddiq as the root of most of Islamic jurisprudence, having a massive influence on Hanafi, Maliki and Shia schools of thought extending well into mainstream Hanbali and Shafi'i thought. Imam Jafar also attained a surpassing knowledge in astronomy and in the science of medicine. it is said that he wrote more than five hundred books on health care which were compiled and annotated by another great scholar and scientist of Islam, Jabir bin Hayyan.

Despite Imam Jafar's abstainment from politics, he was often harassed by the new Abbasid rulers and he was even imprisoned a few times. The reason for this persecution was due to Imam Jafar's popularity, and his standing as a descendent of the Holy Prophet. The rulers feared that he would be able to mobilize against them, and as such they thought it keen to keep him in check.

Once Imam Jafar Sadiq had been summoned by the Caliph who was afraid of his growing popularity and sought some pretext to denigrate and punish him. At last a haggard and slim person entered the durbar and without making the customary obeisance advanced towards the Caliph. To the great astonishment of the entire audience, which expected some harsh words from the Caliph, the latter stood up to pay respects to the learned Imam and seated him by his side. Incidentally the Caliph was pestered by a fly which kept teasing him. He enquired from Imam Jafar:

"What is the purpose of creating flies?"

Imam Jafar replied promptly: "Simply to humble the pride of despots."

The hot-tempered Caliph was all courtesy to the reverend Imam Jafar and when he was leaving, Al Mansur asked him if he could be of any service to him. Imam Jafar Sadiq replied: "The only service I seek from you is that I should not be given the trouble to attend your durbar again."

Many people daily visited Imam Jafar for seeking knowlege from him. Once a person visited him & insisted to see God, Imam Jafar ordered some of his disciples to bind his hands & legs with rope, that person was surprised & tried to run away, but Imam Jafar's disciples over powered him and bound his hands & legs. Then Imam Jafar ordered his disciples to throw this man in the river tigris, they threw him in the rever. That person tried his best to save his life, and finally lost his hope. When he was about to die, Imam Jafar ordered his disciples to take him out. When they took him out & untied him, then Imam Jafar asked him: "Did you see God?" That person replied: "Earlier when I relied on you, that you'll save me from dying, there was a veil on my heart. And when I was about to die, I left myself on God's mercy, so then my heart became unveiled, and now I'm satisfied".

Imam Jafar was a great scholar, he is the founder of "Ilm-ul-Jafar" (which means knowledge of Jafar), Ilm-ul-Jafar is a kind of knowledge that is used to unveil the universal mysteries and to make the use of divine power for specific purposes.

Imam Jafar was died on 765 A.D, possibly from poisoning. He is buried in Madina, in the famous Jannat al-Baqi cemetery.

Once he heard that al-Hakm bin al-Abbas al-Kalbi crucified his own uncle Zaid on a date palm. He was so unhappy about this that he raised his hands and said, "O Allah send him one of your dogs to teach him a lesson." Only a brief time passed before al-Hakm was eaten by a lion in the desert.

Imam at-Tabari narrates that Wahb said, "I heard Layth ibn Sa'd say, I went on pilgrimage in the year 113 A.H., and after I prayed 'Asr I was reading some verses of the Holy Qur'an and I saw someone sitting beside me invoking Allah saying "Ya Allah, Ya Allah..." repeatedly until he lost his breath. He then continued by saying "Ya Hayyu, Ya Hayyu" until his breath was again lost. He then raised his hands and said: "O Allah, I have the desire to eat grapes, O Allah give me some. And my robe (jubba) is becoming so old and tattered, please O Allah grant me a new one." Laith bin Sa'd said that: "He had hardly finished his words before a basket of grapes appeared in front of him, and at that time there were no grapes in season. Beside the basket of grapes there appeared two cloaks more beautiful than I had ever seen before." I said: "O my partner let me share with you." He said: "How are you a partner?" I replied: "You were praying and I was saying Amin" Then Imam Jafar said: "Then come and eat with me" and he gave me one of the two cloaks. Then he walked off until he met a man who said, "O son of the Prophet, cover me because I have nothing but these tattered garments to cover me." He immediately gave him the cloak that he had just received. I asked that man: "Who is that?" He replied: "That is the great Imam, Jafar Sadiq." I ran after him to find him but he had disappeared.

One time someone complained to al-Mansur, the governor of Madina, about Imam Jafar. They brought him before Mansur and asked the man who had complained: "Do you swear that Jafar did as you say?" He said: "I swear that he did that." Imam Jafar said: "Let him swear that I did what he accused me of and let him swear that Allah punish him if he is lying." The man insisted on his complaint and Imam Jafar insisted that he take the oath. Finally the man accepted to take the oath, and he died at the same time.