As a functional food, honey is a food product that is exposed to the risk of food fraud. To mitigate this, the establishment of an authentication system for honey is very important in order to protect both producers and consumers from possible economic losses. This research presents a simple analytical method for the authentication and classification of Indonesian honeys according to their botanical, entomological, and geographical origins using ultraviolet (UV) spectroscopy and SIMCA (soft independent modeling of class analogy). The spectral data of a total of 1040 samples, representing six types of Indonesian honey of different botanical, entomological, and geographical origins, were acquired using a benchtop UV-visible spectrometer (190–400 nm). Three different pre-processing algorithms were simultaneously evaluated; namely an 11-point moving average smoothing, mean normalization, and Savitzky–Golay first derivative with 11 points and second-order polynomial fitting (ordo 2), in order to improve the original spectral data. Chemometrics methods, including exploratory analysis of PCA and SIMCA classification method, was used to classify the honey samples. A clear separation of the six different Indonesian honeys, based on botanical, entomological, and geographical origins, was obtained using PCA calculated from pre-processed spectra from 250–400 nm. The SIMCA classification method provided satisfactory results in classifying honey samples according to their botanical, entomological, and geographical origins and achieved 100% accuracy, sensitivity, and specificity. Several wavelengths were identified (266, 270, 280, 290, 300, 335, and 360 nm) as the most sensitive for discriminating between the different Indonesian honey samples.