The milestone was achieved on the ninth day of the pilgrimage on Friday night. The two-month-long pilgrimage to the cave shrine, located at a height of 13,500 feet above sea level, commenced July 1.
A naturally made ice stalagmite known as "Shivlingam", an icon of Hindu Lord Shiva, is the major attraction for the devotees from across the country.
"Yes, the yatra (pilgrimage) has crossed the 100,000 mark. Till 6 p.m. Friday evening the figure was 99,151, but overnight it crossed the 100,000 mark," an official of the Shri Amarnath Shrine Board told IANS.
Apart from 85 companies (nearly 10,000 men) of the Central Reserve Police Force, 3,000 Border Security Force personnel and soldiers have been deployed for the safety of the pilgrims.
There are two routes to the shrine from Jammu: the traditional route via Pahalgam - and a shorter and steeper one via Baltal.
"This time pilgrims have preferred the traditional route. Around 56,000 pilgrims used the Pahalgam route, as compared to 45,000 who used the Baltal route," the official said.
"It was a delight to be there (shrine). The locals (Kashmiri Muslims) were nice and welcoming," said Sunny Gupta, a young devotee after returning from the pilgrimage.
Fifteen people have died in the Kashmir Valley since June 11 in clashes between protesters and security forces.