Media reports said Thackeray's visit at the temple town is to build pressure on the ruling government, to immediately expedite the construction plans for the Ram Mandir.
More than 2,000 died in widespread riots after the mosque was torn down in 1992.
Many Hindus believe a spot there marks the birthplace of warrior God Lord Ram and that a mediaeval mosque that stood there for 460 years was built only after the destruction of an earlier temple.
The Rashtriya Swayamsevak Sangh (RSS), VHP and Shiv Sena on Sunday organised events in Ayodhya, Nagpur and Bengaluru to muster support for the construction of Ram temple in Ayodhya and mount pressure on the central government to facilitate the temple construction, which is now sub judice in the Supreme Court. The Supreme Court is not giving priority to the case.
"The mosque was a slight on Hindus and it's a shame that we've failed to build a temple on one of the most holy sites for Hindus", said Sharad Sharma, spokesman for VHP, which has close ties with Prime Minister Narendra Modi's Bharatiya Janata Party (BJP).
Hindu groups point to evidence there was a temple there before a mosque was built by a Muslim ruler in 1528.
The calls for the temple construction have regained momentum as the BJP enjoys a majority in national parliament and also in the Uttar Pradesh state assembly.
The issue was also taken to court. The call for the construction of a Hindu temple in Ayodhya has grown particularly loud in the last few months and has mostly come from MPs, ministers and leaders from the BJP.
"But what's worrying is that all this is being given a political colour", he told AFP.
"We're monitoring the entire town by CCTV and drone cameras", Tripathi said.
Ayodhya Municipal Corporation Mayor Rishikesh Upadhyay, however, said there was no fear or apprehension among the Muslims.
No untoward incident was reported from any part of the city.
The Babri Masjid was demolished in December 1992 and since then, the issue of constructing a new Ram Temple has always found its place in the manifestos of the BJP, election after election but the question remains, whether it will be done constitutionally, under the purview of Supreme Court or as per the mob justice.
Both the BJP and VHP and their parent movement, the far-right Rashtriya Swayamsevak Sangh, have asked the government to issue an executive order to build a temple and bypass the Supreme Court.
Zafaryab Jilani, a senior member of the All India Muslim Personal Law Board, said Muslims do not want a confrontation but the state administration must ensure the safety of the community.
Sunday's congregation in Ayodhya would be followed up with bigger gatherings in New Delhi, India's capital, Sharma said.