On November 30, 1970, a massive fire broke out in the temple. It began from the western chuttambalam and raged for five hours. But the Sreekovil (Altar), the Vigraha deity of Guruvayoor, sub-shrines of Ganapathy, Sastha, Bhagavathy and flag-staff remained unaffected. People from all walks of life, irrespective of age, caste, creed and religion fought the fire, setting a glorious example of humanity. Later, the temple was rebuilt.
The incident took place on November 29 during the season of Ekadasivilakku. On this day, Vilakku was celebrated on a grand scale and all the lamps in the Vilakkumatam were lit. After the Seeveli procession, the function came to an end and the gates of the Gopuram were closed. Around 1.00am, somebody who lived near the western chuttambalam saw a blaze within the Temple. As word spread, a huge crowds of people, regardless of religious differences rushed to douse the fire. Later, fire tenders arrived. The conflagration was controlled only by 5.30 am.
Authorities had already removed valuables from the Altar. The Ganapathy deity, Sastha deity and the main deity of Lord Guruvayurappan were shifted to Koothambalam and then to a safer place, residence of the Tantri priest. The fire gutted the whole chuttambalam, the entire Vilakkumatam on the west, south and north. The Chuttambalam was only three yards off, but still the fire did not even touch dry flower garlands, which hung on the corner of the Sreekovil altar.
Two committees were formed to undertake renovation work. One was headed by the Devaswom Minister, Govt. of Kerala and the other was a technical committee to advice on renovation. It comprised eminent engineers, astrologers and Tantrics. The committee arrived at some general decisions
a) To attract more devotees, alterations were made to remove inconveniences as permitted by tantric principles.
b) To increase space for worshippers by reducing the height of Chuttambalam basement. To provide granite pillars instead of wooden.
c) To put granite wall against the Vilakkumatam.
d) To provide a passage around the Ganapathy shrine to eliminate congestion.
e) To reconstruct the Ganapathy temple in granite.
f) To put granite engraved "Ananthasayanam" in place of the old "Ananthasayanam" (Mahavishnu lying over serpent) painting which was lost in fire
g) To widen the gates at the north and east entrances.
h) To reduce the size of the Nivedyathara at the south of the Mandapam.
Eminent astrologers of Kerala were requested to attend the meeting and decide on the Lord's approval for above mentioned changes. Except the widening of two doors, everything else was approved. The foundation stone for the renovation was laid by His Holiness Jagatguru Kanchi Kamakoti Matadhipathy Jayendra Saraswathy Swamikal. The 10 round pillars in the two Vathilmatam were magnificently carved. The eastern pillar on the southern Vathilmatam, at the foot of which Melpathur meditated and wrote the Narayaneeyam was not removed. After the great fire, the temple was reopened on April 14, 1973 (Vishu – Malayali New year).