Two men have appeared in court in connection with the attack on the synagogue in Edinburgh last week, when several window panes were smashed.
Scottish Islamic Foundation chairman Ken Imrie has written to Rabbi David Rose of the Edinburgh Hebrew Congregation to voice the group's "revulsion and horror" at the attack.
"We trust you have adequate security arrangements in place, in line with places of worship across the country. If not, such is our strength of feeling on this matter, we would wish to physically guard the synagogue ourselves," he added in the letter.
It is the second time the Newington synagogue, which serves an estimated 700-strong Jewish community in Edinburgh, has come under attack in seven years and comes amid a reported increase in the number of anti-Semitic attacks in Scotland and across the UK following the recent conflict in Gaza.
The Scottish Islamic Foundation's offer to provide security at the synagogue is intended as a show of strength between the two religious communities in a bid to prevent further unrest.
Mr Imrie wrote in his letter: "We wish you to know that the Muslim community stand full square with you in revulsion and horror at this vandalism. To violently damage any building is wrong. That this is a respected place of worship, faith and spirituality makes the crime even more heinous."
Mosque leaders are to be briefed on the incident so they can echo the sentiments of Mr Imrie's letter during prayers tomorrow.
Rabbi Rose could not be reached last night, but other Jewish representatives welcomed the offer.
Mark Gardner, spokesman for the Community Security Trust, an organisation that protects British Jews against anti-Semitic attacks and helps with other security issues within Jewish communities, last night said Jews had reported a growing number of attacks in recent weeks.
"This was a disturbing incident. Scottish Jews do not expect to experience the relatively high level of anti-Semitism that has occurred during and since the war between Israel and Hamas in Gaza at the turn of the year," he said.
Mr Gardner added that the trust was aware of ten anti-Semitic incidents in Scotland so far this year. The number is what the group would normally hear of in a whole year.
"This statement and others like it around the UK will hopefully encourage both communities to regard each other as allies in the face of racism and extremism," Mr Gardner said.
A man aged 22 and a 17-year-old male appeared at Edinburgh Sheriff Court on Friday on a charge of malicious mischief aggravated by religious prejudice in connection with the incident. They are also accused of possessing a baseball bat at the time.
They both pled not guilty and a trial date was fixed for 8 April.