The objective of the study was to describe clinical and histologic characteristics of eyelid (LMCT) and conjunctival (CMCT) mast cell tumors in dogs and cats presented to a referral clinic in Germany. Medical records were reviewed to identify dogs and cats diagnosed with LMCTs or CMCTs between 2006 and 2020. LMCT were diagnosed in 31 patients and were cutaneous (n = 28; 20 dogs and 8 cats) or subcutaneous (three dogs). Five cases involved the mucocutaneous junction (four dogs, one cat). CMCTs occurred only in dogs (n = 3). At the time of presentation two of the four canine LMCT cases involving the mucocutaneous junction had metastasized to a mandibular lymph node. When applying the Kiupel system, both these cases were categorized as high grade. 85.7% (18/21) of the canine (19 cutaneous and 2 subcutaneous) LMCT and all CMCT cases were categorized as Kiupel low grade. No local recurrences occurred in all LMCT cases in which clean surgical margins were obtained (n = 18, mean surgical margin width: dogs 9.4 mm, cats 3.8 mm). Two cats (2/4) and four dogs (4/7) with questionable or incomplete surgical margins experienced local recurrences (mean time to recurrence of 180 and 637 days in dogs and cats, respectively). Recurrence of low-grade LMCTs and CMCTs following excision with clean margins is rare. Tumors involving the mucocutaneous junction may be of higher grade and prone to lymphatic metastasis.