Yes, there are side effects. They vary depending on the length of treatment (generally patients are not allowed to stay on them indefinitely to mitigate this) and the medication used, but puberty blockers have been used for ~40 years now and we have a good understanding of the risks. GnRH agonists are the most common type of puberty blocker used today, and the typical side effects are:

• Hot flashes
• Gynecomastia
• Fatigue
• Weight gain
• Decreased libido and erectile function

These side effects generally end once treatment stops, whether switching to hormone replacement therapy or stopping all gender-affirming treatment. These side effects are typical of low sex hormone levels in general, and are generally annoyances that can be managed rather than major risks that are likely to harm the patient long term. It's also worth noting that some of these are seen as neutral or even positive to some patients - e.g. patients who were assigned male at birth and are interested in feminizing treatment often consider gynecomastia and decreased erectile function as positive effects.

When puberty blockers are continued for longer periods of time, there are additional risks which grow with the duration of the treatment:

• Reduced bone density, which can increase risk of or worsen osteoporosis
• Metabolic issues, which can worsen weight gain or diabetes in particular
• Having puberty delayed by any means tends to result in a child growing taller than they would otherwise

These risks are more serious, which is why puberty blockers are not prescribed indefinitely. For gender affirming treatment, puberty blockers are generally prescribed for up to two or three years, depending on local regulations and the patient's tolerance of the treatment. After this period, patients have the option of either continuing gender affirming treatment with hormone replacement therapy (so that they can experience a different puberty than the one typically associated with their birth sex), or stopping treatment and allowing puberty to run its course as usual.

It's also worth noting that puberty blockers are not considered in a vacuum - the risks are considered against the risk of allowing puberty to continue as usual. For children with gender dysphoria, puberty is often a severely traumatic experience. This can cause or worsen depression and suicidality, and can leave a transgender person with sexual characteristics they do not want and will have to treat later with riskier and/or more intense forms of treatment like surgery. The risks of puberty blockers are comparatively mild, which is part of why the side effects are regarded as safe for transgender patients.

Lastly, I'll also note that all of this treatment involves mental health professionals as well. While adults in some regions can choose to start gender affirming treatment on their own without needing a formal diagnosis, treatment for children requires much more work and dedication. Typically, a minor who wants to begin gender affirming treatment for gender dysphoria will need:

• Consent from at least one parent
• A diagnosis or letter of support from a mental health practitioner who's seen them as a patient
• A doctor or endocrinologist who can prescribe the medications
• Ongoing check-ups while they're undergoing treatment, to assess both their physical health (physical exams, blood work to check hormone levels and organ function) and mental health (sessions with a mental health practitioner to make sure that the treatment is actually benefiting their mental health and consistent with their identity)