In the 16th-17th centuries, a small monastery was located on the territory of the modern architectural complex, which includes the churches of Elijah the Prophet and Varlaam of Khutyn. It was closed in 1738. Until 1780, there was a small stone church on the site of the Church of Varlaam of Khutyn, which was completely dismantled and rebuilt.

The modern Church of Varlaam of Khutyn demonstrates the influence of early St. Petersburg classicism, which began to spread in Vologda in the late 18th century. It can be assumed that it was designed or built by a talented master from the capital, as evidenced by the carefully crafted decorative details and the elegant bell tower. The uniqueness of the church's architecture among fifty others in the city, except for the Church of Nicholas the Wonderworker on Sennaya Square, supports this assumption. However, the presence of buildings in a similar style in Vologda suggests that the architect could also have been local.

The Church of Varlaam of Khutyn has two floors and is small in size. The western facade with the main entrance is adorned with a semi-rotunda supported by four Ionic columns. Above it rises a tall square bell tower with concave faces and corners, decorated with Corinthian columns and pilasters that support a light frieze. The bell tower is topped with a complex pyramidal dome with a slender spire. The dome over the eastern part of the building is designed as an oval lantern with a small cupola. Decorative vases with stucco garlands on pedestals, serving as two other domes, give the temple a secular character.

The overall appearance of the church is somewhat marred by a wide buttress added in the mid-19th century on the left side of the rotunda. The left part of the temple has moved away from the bell tower, which is integrated into the building, resulting in a crack and the need to reinforce the side wall. Aside from this extension and other minor changes, the exterior of the temple has been preserved in the form it had in 1780, which cannot be said about its interior decoration. A notable feature of the temple is the 'confessional space' in the southern part of the altar, which is not found in many churches.