The aim of the study was to identify the frequency of loneliness and to examine the factors associated with loneliness among homeless individuals in Germany during the COVID-19 pandemic. Data were taken from the 'national survey on the psychiatric and somatic health of homeless individuals during the COVID-19 pandemic'. The data collection took place from 26th July to 17th September 2021 (the analytical sample included n = 491 observations). The well-established UCLA-3 tool was used to quantify loneliness. Independent variables included sex, age, marital status, the existence of children and pets, level of education, country of origin, duration of homelessness, alcohol and drug consumption, mental health concerns and concerns regarding COVID-19 illness. Multiple logistic regressions were used to examine the predictors of loneliness. The frequency of loneliness was 41.7% for the total sample. Multiple logistic regression analysis stratified by gender showed that a higher likelihood of loneliness was associated with being born in Germany, being middle aged (40 to 49 years compared to 18 to 29 years), having mental health problems and a short period of homelessness (1 month compared to longer periods) among women. In men, a higher likelihood of loneliness was associated with a higher fear of COVID-19 and a short period of homelessness. Our study revealed a high frequency rate of loneliness among homeless individuals. The study results highlight the associations between some explanatory variables (i.e., the duration of homelessness and mental health problems). Identifying the factors associated with loneliness may help to adequately address the problems of homeless individuals at risk of loneliness. Longitudinal studies are required to confirm our findings.